Trufa on Broadway is fantastic! It's delicious, high quality, affordable, with a great atmosphere (it's tiny but i've never had to wait) and they use organic and free range ingredients! I cannot say enough good things about that place.
Not sure if it counts as Hamilton Heights since it's down the hill, but Covo on 12th ave (a few blocks North of Fairway) is a beautiful Italian restaurant. It's a bit pricey but worth the money, especially on a date or special occasion.
Lots of people go to Picante (also on Bway) for Mexican food and a fun night scene.
