These should be the glory days for Ray Kelly. His years as New York police commissioner—13 in all and the last 11 since 2002—have seen crime rates plunge, the murder rate hit a historic low, and several foiled terror plots since 9/11 but no successful attack. The last time the city felt this safe, the Dutch were raising cattle at the bottom of Manhattan.

So why are Mr. Kelly and his officers suddenly under ferocious political assault?

The liberal candidates—there is no other kind in these parts—are whacking with particular gusto at a police tactic called “stop-and-frisk.” The practice involves stopping people who behave suspiciously, questioning them and, if they appear to present a threat, frisking them to see if they’re carrying a weapon. The accusation is that this age-old police tactic unfairly targets minorities.

Surveying the current Democratic candidates, Mr. Kelly explains their basic campaign strategy: “You suck up to a special-interest advocacy group.” One such group is the Center for Constitutional Rights, which is suing the NYPD in federal court to stop stop-and-frisk.

An audiotape recently played at that federal trial featured police commanders who were secretly recorded by an officer who has complained of discrimination. When the complaining officer asks if he should stop “every black and Hispanic” in a particular minority neighborhood, one of the commanders rejects the idea and says that in that neighborhood, the suspects in a recent series of robberies and larcenies were “male blacks 14 to 20, 21.” Elsewhere on the recording, the same commander says, “The point here is that 99% of the people in this community are great, hard-working people who deserve” a safe neighborhood. Another supervisor tells the subordinate not to accost people without cause but to question people who appear to be “doing something wrong.”

In some local media outlets, the recording was presented as evidence of racial profiling. “They are hellbent on finding anything they can wrong with the department,” says Mr. Kelly of his press critics.

The profiling accusation is especially galling to the 71-year-old former Marine and Vietnam vet. “We have transformed this police department,” Mr. Kelly says. “We’ve made major changes in the last decade. For instance, the police-officer rank is majority minority. Nobody knows that. You can’t get that story out.”

Another story that doesn’t get out is the astonishing transformation of New York City over the past two decades. In 1990, there were 2,245 murders, a record. There was a sense of menace in every borough and on the subways. A 10-year-old girl was strangled to death. A 22-year-old tourist was killed defending his mother against a gang of muggers. Dozens of New Yorkers were killed by stray bullets.

Since that terrible year, the annual number of murders has fallen more than 80%, to 419 in 2012. If the 1990 murder level had been maintained for the past 23 years, the rough math suggests that perhaps 40,000 New Yorkers—most of them black and Hispanic—wouldn’t be alive today.

The revolution in safer streets occurred even as the city was adding more than a million new residents—to 8.4 million today—since 1990. Completing this tale of rare government success, Mr. Kelly notes that the current police force of 35,000 has 6,000 fewer officers than when he became commissioner in 2002.

Mr. Kelly says that stop-and-frisk is a critical—and constitutional—part of this success. “We put our officers right in the middle of where the problems are, mostly minority areas,” says the 43-year veteran of the NYPD. “You develop very quickly a sense of who’s doing right and who’s doing wrong—and who’s carrying a gun.”

What counts as suspicious? Mr. Kelly mentions “scouting out a car, or following people.” Or several young men waiting outside a bodega near closing time, or standing in the shadows near an ATM.

As Mr. Kelly describes it, when a police officer observes such activity, he is allowed to approach people and “ask them the nature of their business, what they’re doing.” He says this is legal under New York law and in “virtually every other jurisdiction in America.” If the officer then feels threatened, he is permitted to do a “limited pat down” of the potential suspect. And if the officer feels something that he believes is a weapon, he can conduct a “full search.”

In trying to spot the troublemakers before shots are fired, are the police unfairly targeting minorities? The commissioner says the data suggest that blacks are “under-stopped significantly,” while other ethnic groups are “over-stopped.” He reports that 53% of stops involve African-Americans, though blacks commit more than 70% of crimes. Hispanics on the other hand make up 32% of stops but commit 26% of crimes.

The top cop adds that even if his department is taking heat from the left, police stops of suspicious characters are popular where likely crime victims live. After all, 96% of shooting victims and 90% of murder victims in New York City are black or Hispanic.

“I was in a black church this Sunday. Standing ovation,” Mr. Kelly says. “They know they’re being victimized. They know crime has gone down in the black communities and they are very much concerned about it going back up.”

The court case has him concerned about the potential loss of a powerful deterrent. “If you don’t run the risk of being stopped, you start carrying your gun, and you do things that people do with guns. And you see what you have in some other places in this country.”

Could crime-riddled places like Chicago learn from New York’s example? “People come here and look at what we’re doing all the time, and we have manuals. I think the biggest difference is political support,” Mr. Kelly says. He believes that the “steadfast” backing of Mayor Michael Bloomberg is the key ingredient in the department’s success—and derives partly from the mayor’s vast personal fortune. “If you are an ordinary politician and you’re counting on campaign contributions, the pressures are different.”

The mayor has joined Mr. Kelly in criticizing a recent proposal from Democratic mayoral front-runner Christine Quinn to create a new inspector general to oversee the NYPD. The department is already overseen by two independent city agencies, plus the five district attorneys and two U.S. attorneys based in New York City. Mr. Kelly views the additional layer of bureaucracy as “totally unworkable” and says he already runs an organization with more oversight “than any police department in America.”

Meanwhile, the stop-and-frisk case continues in the federal district court of Judge Shira Scheindlin, while the Brennan Center at New York University and the New York Civil Liberties Union keep pressure on the mayoral candidates to turn left. “It’s just a small group and they have intimidated these politicians to take this route. And also, in my view, the judge is very much in their corner and has been all along throughout her career,” he says, again with calm if surprising candor. If police can’t do stops, he says, “you’d need another 50,000 cops” to protect the city.

“I think one of the biggest scams in law enforcement is the monitor,” Mr. Kelly says. The plaintiffs in the stop-and-frisk suit have demanded such an overseer to watch the police. Mr. Kelly describes how the practice has worked under an “extremely aggressive” U.S. Justice Department going “around to different cities,” where “they’ll find some sort of discriminatory pattern in their minds.”

The feds threaten to sue the cities unless they agree to a civil-rights monitor, and most cities agree, to avoid the cost of litigation. “So it’ll be a politically acceptable lawyer who will be put in there and will always find something wrong, because they get paid. A city like Detroit pays, I don’t know, a couple million dollars a year, whatever, to this firm and guess what? Nothing is ever right, because if I find everything’s right then I stop getting paid.”

So apart from stop-and-frisk, what are the other secrets to anticrime success? He partly credits an increasing focus on youth gangs and the way they communicate. “There is a social media component, because these kids, these crews, are bragging and telegraphing what they’re going to do in terms of who they’re going to shoot, who they’re going to kill. They go in front of the [intended victim’s] house and they’ll stand in front of it and get a picture. And they try to play a game with code. But we break the code.”

If only terrorists were always dumb enough to leave Twitter clues. Mr. Kelly’s tenure has also been marked by the lack of a successful terror attack. The NYPD’s 1,000-strong counterterrorism force works closely with Washington, and Mr. Kelly is concerned about a possible lowering of the federal guard.

“If you look at the latest National Intelligence Estimate,” he says, the Central Intelligence Agency and the Department of Defense “are sort of now downplaying the threat of terrorism. . . . They look back historically, ‘Hey look how few really big events we’ve had.’ Meantime, I see New York City differently. We’ve had 16 plots against the city.”

One recent example: Quazi Mohammad Rezwanul Ahsan Nafis, who “thought he was blowing up the Federal Reserve Bank” of New York as part of an FBI sting operation, the commissioner says. “He goes to the New York Stock Exchange, sees the police that we have there and he decides he can’t do it. Too much security.” So the suspect instead parked what he thought was a van full of explosives in front of the Fed and tried to detonate it from a distance with a cellphone.

“There are other investigations of young people like this that are ongoing right now,” says Mr. Kelly. “We see ourselves as the number one target and we have this stream of young men who want to come here and kill us.”

Media reports have suggested that his department unfairly monitors the Muslim community—the Associated Press ran a Pulitzer Prize-winning series on that score in 2011. Asked what he has changed about the NYPD’s surveillance methods in the wake of those stories, Mr. Kelly says: “Nothing.”

An old judicial consent decree, modified after 9/11, lays out exactly what the police are allowed to do in gathering public information that may help prevent terrorism, he says. The department follows these rules. Next question.

OK, here’s one: Will Ray Kelly jump into the mayoral race and take on his critics? On the recent church visit where the crime-fighter was so warmly received, many of the congregants urged him to run. But Mr. Kelly notes that a certain woman named Veronica, his wife of 49 years, opposes the idea. Many New Yorkers are hoping she’ll reconsider.