I stayed here...
http://www.theroosevelthotel.com/
Rooms quite small (though quite common in NY) and no frills but did us fine and about 10 mins walk from Time Sq and very handy for 5th Avenue etc... Got a great deal on Expedia.
We had breakfast each morning in this fab diner...
http://www.menupages....urants/the-red-flame/
We walked everywhere save for one trip on the subway. Day one we did the Empire State early (so much quieter!) walked up 5th Ave via Tiffany etc... up to Central Park (you can turn off to Bloomingdales just before too) and went to the zoo in there and round the park and then Top of The Rock (amazing at night!).
Day 2 we walked down 5th (passed Macys etc...) through Greenwich Village, Little Italy and China Town, past ground zero, Wall St then on the Staten Island Ferry (great free way to see the Statue of Liberty) then back then subway back up - it's a LONG walk!
Day 3 we got one of the bus tour passes and did the downtown tour stopping midway to hop on the Brooklyn one where they dropped us back off by the Brooklyn Bridge (buses can't go over it) so we could walk back over (it's quite a walk) and rejoin the downtown tour, then did the uptown tour inc Harlem then back and on the night tour where they take you to the Hulton Ferry Landing to see the NY skyline all lit up at night.
Enjoy, it's a fantastic city! Just remember to get into the tipping culture.