I definitely agree with Eataly! We just went last week (try to go on a weekday- I heard the weekends get crazy). It was nice and quiet on Thursday and the food was sooooo good. Thursday they have porchetta at the little sandwich shop inside and it is to die for. I have a ton of pics posted on my blog if you take a peek (highly-experimental.blogspot). We also ate at Ma Peche- super tasty, but pricey. Their menu is online, this is one of David Chang's restaurants and we really enjoyed it.
Bond 45 had nice Italian and they are super fast if you are going to a show- however, they weren't anything "special", so not at the top of my revisit list.
Late night is fun at Chez Josephine (named for Josephine Baker)- they have live music, kind of cajun, New Orleans style with lovely french food. Another late night spot we enjoyed was the Stanton Social Club- I believe it's in SoHo. It was mentioned on the Best Thing I Ever Ate on FN because of the onion soup dumplings. Super tasty but be careful- you can burn the heck out of your mouth! Also very creative and interesting drinks.
Have fun in NYC- we can't wait to go back...