I have taken a helicopter trip around NYC 3 times and each time has been great. The best time is at dusk on a clear night.
EWR is fine for me also. BA have a lounge there and it is quite quiet and easy to get through.
Hotels, well that is tough. The Waldorf is great IF you get a good room and crap if you don't. I like the Hilton Time square for the modern rooms and the location. Just book two rooms.