Stayed at Liberty Harbor in 2006. It was very convenient to the subway
(about a 3 block walk) and was tight, but we only needed a place to stay the night. We spent 9 days there and did the U S Open Tennis and a tour of New York City.
There may be others, but this place is ok. When we were there, they had a night watchman in a tower who scared us when we came in one night at 2 AM. Even though it is a little high, I would recommend this place because of the convenience to NYC.