Authorities say 19-year-old Manuel Riquelme approached 28-year-old Eugene Lovendusky, yelled a slur at him and punched him in the jaw.
Lovendusky's glasses were knocked off, but he declined medical attention.
Riquelme was caught at a pizzeria at West 40th Street and Ninth Avenue.
Lovendusky, of Queens, is the co-founder of Queer Rising, an LGBT rights and advocacy group.
He had left the XL nightclub and was walking to the subway with two friends at the time of the attack.
Police Commissioner Ray Kelly praised the increased reporting of anti gay bias attacks.
"I can tell you that after the terrible events in the sixth precinct, there was a lot of notoriety given to it," Kelly said. "And we believe that these types of bias crimes are under reported. So this is something you may well not have heard about. But now it's being reported, and we think that's a good thing. The first thing we want to tell the victims is to report it. We have to know about it before we can take action, and this is an example of action has been taking. "
Riquelme was charged with assault as a hate crime and harassment.