A couple of years ago we stayed at the Wolcott (
http://www.wolcott.com) and booked our flights and hotel through expedia. We got a week for less than �500 which included flights, hotel and breakfast. It was also walking distance from Times Square and Central Park (although a bit of a trek).
The price will probably have gone up a bit but it was still the best value when we were travelling. It was in need of an update decor wise and one of the two lifts was out of order, but it was clean, comfortable and with it's own bathroom