I stayed in the Roosevelt as a good deal with flights on Expedia I think.
It's the one at the end of Maid In Manhatten. Rooms were small though I understand that's common in NYC and was fine for the two of us. It was 10 mins walk from Time Sq/Grand Central.
http://www.theroosevelthotel.com/
We didn't breakfast there, we went to a diner called the Red Flame which was great - typical brusque, but friendly, NY service but quick, great food and reasonable prices and not ridiculously large portions like some places.
http://menupages.com/...urants/the-red-flame/
Take lots of change for tipping and get a good feel of how much to tip for what as it's a huge tipping culture and is expected - you're often told if they don't think you are tipping enough! Watch the hotel staff as they will take any opportunity to grab and carry your bags etc... then demand a tip for it.
Empire State early morning is best before the queues and allow time as even without a big queue it takes a while to get up there with a few stages and security scanning. Top of the Rock (Rockerfeller Centre) is great at night.
The bus tours are great value and many of the guides are brilliant and really knowledgable. We got a 24 hour package and did all the tours on our bus in a day (downtown tour down then grabbed the Brooklyn tour, walked back over the Brooklyn Bridge, did the rest of the downtown tour then did the uptown tour including Harlem then the nightime tour when you to go the Hulton Ferry landing to see the skyline at night.
We also walked from our hotel to Time Square then right down 5th Avenue taking in the Garment District, Macys, Flat Iron Building, Greenwich Village, Little Italy (lovely for lunch outdoors), Chinatown, Ground Zero, Wall Street then got the Staten Island ferry there and back to see the Statue of Liberty and view back for free. Got the subway back, very long walk but you get to see so much.
Also note it may be very hot and humid there in the summer.
Enjoy, it's an amazing place!