We are going in May, and we are staying in Long Island City, which is closer than Jersey City, bu twith the same benefits in terms of bigger rooms and lower prices. We are right near a station, (comfort inn, I believe ) and my cousin, who lives in Manhattan, said that we will be in most places in just a few minutes from there. Size of the Manhattan hotel rooms were an issue for us, since we are a family of five, and almost all of the hotels in Manhattan were $300 and up a night. LIC hotels were bigger, about $150 a night (some less!) and most included breakfast.
Did you know about the free nights for the 9/11 exhibit? I think it's on Tuesdays, and you have to reserve them in advance. We won't be there on a Tuesday, but that would have been a huge savings for us. The Trip Advisor forum has been a wealth of info for me planning our trip. Have fun!