JFK is approx the same distance from the pier and staying in Manhattan would be very convenient. Be prepared for among the most expensive hotel pricing in the world there or to stay in a dump if you want affordable. That's about the only two choices.
Re-read my last post. For reasons of economy only, you can get a hotel across the river for rates competitive with most of the nation, with national chains you've heard of with nice rooms large enough to get out of bed without scooting to the end of the bed. Then opening the door before stepping out of bed so you can actually open the door to the hallway or bathroom, some reall are that small. That is, if you can find an affordable hotel in NY that actually has a private bathroom in your room. NYC has pricey Real Estate and high taxes, as a result very high cost for hotels in the city or in Manhattan especially.