NEW YORK — New York City’s police commissioner is retiring after three years, and a top deputy will succeed him as the leader of the nation’s largest police department, Mayor Bill de Blasio said Monday.

James O’Neill, 61, moved the police department away from controversial “broken windows” policies and oversaw continuing drops in crime. He will remain on the job until next month, when he leaves for a job in the private sector.

Chief of Detectives Dermot Shea, a 28-year department member who started as a patrolman in the south Bronx, will be the new commissioner. Shea rose to prominence as the department’s statistical guru, and de Blasio said he is “one of the best-prepared incoming police commissioners this city has ever seen.”

“He knows this department inside and out,” de Blasio said. “He knows this city inside and out.”

O’Neill’s tenure as commissioner — which began with a pipe bomb blast on his first full day in office in September 2016 — came as the city continued to grapple with its place as a top terrorist target, as well as tensions between officers and the community.

“We’ve redefined in these last six years how we police this city,” Shea said at a news conference on the leadership change. “We have done what many thought was impossible. We have pushed crime down. We have reduced incarceration.”

O’Neill moved the department from a focus on the broken windows theory, which viewed low-level offenses as a gateway to bigger crimes, to a neighborhood policing model designed to give officers more time to walk around and interact with people in the communities they police.

He led the department’s response to a truck attack that killed eight people on a Manhattan bike path in 2017 and brought closure this summer to one of the NYPD’s lowest moments in firing an officer in the 2014 chokehold death of Eric Garner.

O’Neill said the decision in August to fire Officer Daniel Pantaleo after five years of investigations and disciplinary hearings weighed heavily on him and the department. The city’s largest police union responded by calling on O’Neill to resign.

O’Neill said Monday the firing wasn’t a factor in his decision to leave. He felt this was the right time to leave, he said.

“This job comes with a lot. It comes with a lot of pressure,” he added. “This is all I have thought about for the last 38 months — 24 hours a day, 7 days a week. It’s all you think about, is keeping the people of this city safe, and it was an honor to serve.”

De Blasio’s sudden move to install Shea, the son of Irish immigrants, as O’Neill’s replacement was not without criticism. Tina Luongo, of the Legal Aid Society, said there should have been an open, transparent process with input from city residents.

Under Shea, Luongo said, the police department has expanded its database of alleged gang members — often black and Hispanic men and women — and codified expansive DNA collection practices.

“This will be more of the same, and our clients — New Yorkers from communities of color — will continue to suffer more of the same from a police department that prioritizes arrests and summonses above all else,” Luongo said in a statement.

Shea last year oversaw an overhaul of the special victims division, which deals with sex crimes, including the ouster of the chief in charge when Harvey Weinstein was arrested in 2018.

Under new chief Judith Harrison, the division has added several dozen more investigators, retrained staff and shifted how rape statistics are reported to the public. But some victim advocates called for Shea’s resignation, saying the changes aren’t enough.

“We hear the advocates. We’re not done,” Shea said. “Sexual assault survivors are of the utmost importance to us.”

O’Neill joined the NYPD as a transit officer in 1983 and spent more than three decades with the department before being appointed in September 2016 to replace broken windows proponent William Bratton as commissioner.

In that role, O’Neill led efforts to bolster community policing and repair the department’s relationship with minority communities that had complained about innocent black and Hispanic men being caught up in aggressive enforcement of minor crimes.

The past year has been particularly trying for O’Neill, with two police officers killed by friendly fire and a rash of suicides by police officers leading him to declare a mental health emergency.

Since mid-October, NYPD officers have shot five people, killing four of them. In one case, an officer was shot at and saved by his bulletproof vest. In another, an officer was slammed in the head with a metal chair and spent several days in a medically induced coma.

At times during O’Neill’s tenure as commissioner, it appeared he was caught between loyalty to his men and women in blue and the progressive policies embraced by his boss, de Blasio, and pushed by police reform advocates.

In one example, O’Neill said he wanted some changes to a state law that keeps police disciplinary records secret, so the department could share outcomes of cases with the public, but did not support a full repeal.

Asked in recent weeks about rumors of his retirement, he said he had the “best job in the world.”

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