Greg Kelly, son of NYPD Commissioner Ray Kelly, accused of raping woman in her office

'Good Day New York' co-anchor Greg Kelly with his father, NYPD Commissioner Ray Kelly.

Alleged attack occurred Oct. 8 after two had drinks at the South Street Seaport

A Manhattan woman has accused “Good Day New York” co-host Greg Kelly - son of Police Commissioner Raymond Kelly - of raping her inside her Lower Manhattan office last October.

The woman told cops she had drinks with Kelly, 43, at the South Street Seaport Oct. 8 before he sexually assaulted her in the law firm office where she worked, sources said.

The accuser, who is around 30, did not report the alleged sexual assault until Tuesday night, when she walked into the 13th precinct and gave her account, sources said.

Cops interviewed the woman, but because of the conflict created by probing the commissioner’s son, they quickly turned the case over to the office of Manhattan district attorney Cyrus Vance.

The commissioner became aware of the accusation against his son when a man, claiming to be her boyfriend - apparently enraged over the alleged attack - recently approached the commissioner at a public event.

“He said, ‘your son ruined my girlfriend's life,” said NYPD spokesman Paul Browne. “The commissioner said 'Well, what do you mean?' He said he didn't want to talk about it here so the commissioner told him to send a letter."

Browne said he was unsure if the man ever sent a letter.

The woman told cops she met the younger Kelly on the street at some point before they met for drinks, sources said.

It was unclear why she waited more than three months to make a report.

The woman, who had invited the anchor back to her office, continued to have contact with him after the alleged rape, a source said.

“There was communication of some kind,” the source said.

Greg Kelly denied the rape allegation through his lawyer, Andrew M. Lankler.

“Mr. Kelly is aware that the New York County District Attorney’s office is conducting an investigation,” Lankler said in a statement. “Mr. Kelly strenuously denies any wrongdoing of any kind, and is cooperating fully with the district attorney’s investigation. We know the district attorney’s investigation will prove Mr. Kelly’s innocence.”

Lankler said he did not expect prosecutors to take any action this week.

A spokesman for Vance declined comment.

Kelly, a Marine-turned-journalist, became co-anchor of Ch. 5's "Good Day New York" in 2008.

He has endeared himself to early-rising New Yorkers for his on-air camaraderie with co-anchor Rosanna Scotto.

His previous assignments included covering the Iraq war and the White House for Fox News Channel.

Kelly spent nine years as a fighter jet pilot in the Marine Corps, making a 158 aircraft carrier landings and flying over Iraq to impose a no-fly zone, according to his work biography.

The Fordham University political science grad is a licensed commercial pilot - and Lieutenant Colonel in the Marine Corps Reserves, his bio says.