New York’s top cop made a historic apology Thursday for the violent NYPD raid at Greenwich Village’s Stonewall Inn 50 years ago that catalyzed the modern gay rights movement.

“The actions taken by the NYPD were wrong, plain and simple,” Commissioner James O’Neill said of the June 28, 1969, police raid on the now legendary Christopher Street gay bar.

Cops that night slammed patrons against walls, hurled insults and swung billy clubs as the club was raided under the pretext of liquor law violations — leading to protests and violent clashes with police.

“The action and the laws were discriminatory, and oppressive, and for that I apologize,” O’Neill said.

The commissioner also made a “vow” to the LGBTQ community, saying “that this would never happen in NYPD 2019.”

“We have and we do embrace all New Yorkers. We are a department that is inclusive,” he said.

“We are at the beginning of World Pride Month. And I want nothing to detract from this inspiring celebration. In both my personal and professional life, I do my best to act responsibly.”

O’Neill made the apology during the inaugural Pride Month safety briefing attended by LGBTQ community leaders and advocates — and a day after City Council Speaker Corey Johnson called on the NYPD to issue the mea culpa ahead of the 50th anniversary of the Stonewall uprising.

O’Neill had refused to apologize when asked to in 2017; his predecessor, William Bratton, had also refused to apologize.

Johnson responded Thursday with a tweet of thanks.

“We appreciate this apology. Thank you @NYPDONeill. This is so wonderful to hear during Pride,” he wrote.

The official Twitter account for New York City Pride also tweeted a “thank you” to O’Neill and the NYPD.

“We are all very proud today!” the tweet read.

Stonewall Inn co-founder Stacy Lentz, who attended the briefing at 1 Police Plaza, told The Post that the apology “has been a long time coming.”

But a group called the Reclaim Pride Coalition, which is holding the Queer Liberation March later this month, slammed O’Neill for his “empty apology,” complaining it was “given under pressure during Pride Month.”