Go back from new york last month (honeymoon too), some good ideas above.
I agree with klunky, the new york pass is really good value for money, well worth checking out.
Things to do;
Top of the rock (dont bother with the Empire), great views of the city
Boat trip around Manhattan, takes about 3 hours. The guide was excellent and very informative. Best part of the trip!
Ellis Island, allow half a day or so to go around the museum on immigration.
Intrepid museum, well worth a visit if you like aircraft, my wife cant stand aircraft but enjoyed the museum.
Where to eat;
Best two places where Blu Fin (By red stairs/theatre ticket office in Times square on the west side). Excellent breakfast.
Johns pizza place (we went to the one off Times Square
http://www.johnspizzerianyc.com/index2.htm
And on a sad/geeky note, if you’re a coffee drinker, go to Starbucks and get a large coffee flask. The staff in the UK cant even get hold of these and it makes the jealous 😀
Enjoy, wish i could go back