Top of the rock do a ticket that lets you go up twice in the same day, worth it.
I only went up the Empire State once, but it was late afternoon and I watched sunset from up there.
USS Intrepid was worth a look around, they have a space shuttle there right now. I don't know if its open or not - sustained damage in the hurricane and was shut.
As someone said, go out for breakfast every day, when I came back I was proper grumpy for a few days because I couldn't just drop in somewhere and grab some breakfast and a coffee
Go for a walk in Central Park in the snow.
Its worth going to Liberty & Ellis Islands just for the view of lower Manhattan.
Far as bargains go, I very much doubt it, especially at that time of year.
Walk as much as you can, its a great city to walk around.
Pics from January
http://www.flickr.com/photos/hotrods/sets/72157629058938023/
USS Intrepid
http://www.flickr.com/photos/hotrods/sets/72157629070450429/