I live in New York, so I might be able to help. Don't stay on Long Island, it's too far from the city. Hotel rooms are going to be more expensive in summer than any other time of year, except around Christmas/New Year's when they are equally high. Additionally, the weak value of the dollar has brought droves of Europeans to New York this summer. Occupancy rates have been better than they have been in years. Consider staying in New Jersey, especially in Hoboken or Jersey City. There is a Hyatt on the water in Jersey City that a lot of people stay at that is convenient to Manhattan without the city prices. Both areas are easily accessible to the PATH train system. PATH, or Port Authority Trans-Hudson is a safe and reliable "subway" system that connects mid-town, Chelsea, Greenwich Village, and the World Trade Center to Newark, Hoboken, and Jersey City. The fare is $1.50 per person, each way. If you insist on staying in the city (what New Yorkers refer to as Manhattan) you will pay more to be near the tourist areas of midtown, Chelsea, the west village, and the upper west and east sides (of Central Park). You will also find higher prices in the Brooklyn Heights and Williamsburg areas of Brooklyn, which are right across the East River. If you can find a hotel brand you like that has a property in the Washington Heights area of Manhattan (the far north of the island) you might get good prices there. Also, Harlem is becoming a safer more upscale area than years past, especially now that Clinton's offices are there. Becareful, however, that Harlem still has some rough areas. You might also consider the area around Columbia University and the main campus of Columbia/Presbyterian Hospital which is north of Central Park. If it were me, I would stay in Hoboken. It has become quite trendy and somewhat upscale without the equivilent prices...yet. Hoboken is a university town (again, right across the Hudson from the city) and hasn't been hit by city prices. The areas along the waterfront in Jersey City and Hoboken have wonderful areas to stroll and the views of the Manhattan skyline are some of the best anywhere. Have a good time.
If it pisses off the right, I'm all for it.