DW and I will be in NYC for the first time for 3 nights in March (3/29 - 4/1).
It's our first kid-free trip in 12 years, so we're super excited.
We're actually going to 2 shows, so we decided we definitely wanted to be near the theaters. Right now, we have reservations at the Michelangelo. Our neighbor, who grew up in Manhattan, recommended it. The regular rates are very high, but we got a special winter rate, so we're paying $295 on Thurs and $240 on Fri and Sat nights.
www.quikbook.com seems to have some really good rates on NYC hotels and most of them are fully refundable/cancellable. I used tripadvisor.com to read reviews on hotels when I was researching. travelzoo.com is also a good site, but most of their deals are only for the next couple months. I'd suggest using quikbook or another site and booking something now that can be cancelled. Then as the trip gets closer, you can keep your eye out for better deals.
Obviously I'm not an expert, but just a couple suggestions I've been given. Top of the Rock is supposed to be just as good as Empire State Building, but less crowded and shorter wait times. Also, if you just want to see the Statue of Liberty, but don't care about going in and don't want to spend the whole day doing it, a ride on the Staten Island ferry supposedly gives you a great view and is free (or very cheap)