Sharif Mitchel, 29, of the Bronx, has been charged with stalking and harassment, among other charges.
Police say a woman got on the northbound No. 2 train at 42nd Street and Times Square around 3 a.m. As the train left the 72nd Street station, a man sat next to her.
He began to compliment her, and started to touch her right leg, according to police. When she asked him to stop, he pointed a gun at her.
When the train reached the East 149th Street and Third Avenue station, the man told the woman to get off the train with him, police said. She refused.
Police say he then left the subway, and the woman got off at the Intervale Avenue and White Plains Road station, along with two Good Samaritans who saw part of the confrontation. They called police.
The suspect was stopped in the 2600 block of Third Avenue, and identified, in part, by a Playboy bunny tattoo the victim had noticed. He was arrested.
A gun was recovered from the suspect's front pants pocket, along with a loaded magazine from his pocket.