Was there in August last year, used http://www.zagat.com/newyork for resturants, pretty spot on, went to Cafe Loupe in West Village which was great.
Also went to an italian place just off time square that did the biggest portions I have ever seen. Not a birthday place but was worth a visit just for the waiter experience... No menus, they just recite it too you!!
Spent a fair few hours in a bar off time square that was owned by Mohammed Ali's trainer, and had a beer with Ricky Hatton who happened to turn up for a chat with him... Which was nice! Trying to remember the name!
Stayed in the The Iroquois Hotel which I can highly recommend. Great location and everything you need.
Love the city and cant wait to go back!
Oh and get the ferry to statten island, makes it feel like your in a film! And your Mrs will get the Sex in the City feeling!!