I usually go to Ciel bikes. Cool guys, good service, good mechanic work.
Bike Works NYC is pretty decent.
King Kog has pretty good stuff but IIRC they're kinda jerks. I went in and there was one guy behind a counter staring at a magazine who completely ignored me. There's no way he didn't see me since the place is about the size of my living room.
There's Affinity which has a decent rep.