I would suggest the Lincoln Harbor Sheraton a PP linked to above. It has ferry service right into the city, a spectacular view of the skyline, and its restaurant is pretty good.
If you're pricing things out on-line, be sure to include Secaucus in your search. It won't be as convenient to public transport as the Lincoln Harbor, but some properties run their own shuttles into the City and you could score a good price there. The Embassy Suites there is really nice.