You might want to consider 'inoteca Gramercy. They serve the full menu in the dining room until 1 a.m. We had a very late supper there a few weeks ago on a Tuesday, and the food was excellent. The dining room was virtually deserted at 11 p.m. Though there was music playing, we enjoyed the overall peace and quiet especially since, when it's busy, the noise level is deafening. We've never been to Balthazar that late, but I'm guessing it would be more lively.
I would try:
Balthazar (I think they take reservations pretty late on in the evening)
Blue Ribbon Brasserie (bit of a wait)
Spotted Pig (ditto)
A lot of Japanese places stay open pretty late, not sure if that's what you're looking for, though. Yakitori Totto? Sushi Seki?