New York has more gay bars than any other city in the world. What is your scene?
We may go out to a night club, but I am referring to a daytime bar where you can go and have a nice conversation and is more laid back.
First, keep in mind that New York is not really and "early" city and before Happy Hour they are not very crowded.
In the East Village: Nowhere Bar, Phoenix and Boiler Room. The Cock if you want some late night naughtiness...
In Chelsea: Gym Bar, Barracuda and XES. The owners of the long-missed Hell opened a place called Secret that is supposed to be good but I have not been there yet.
I shall second Phoenix and Gym Bar. Boxers is also usually pretty fun.