JFK is a better choice, and if the OP is interested in going outside NYC to stay, they could take the Airtrain to Long Island too..
Or they can take the Airtrain from JFK to Jamaica and either take the LIRR to Penn Station, or the subway into Manhattan, Queens or Brooklyn.
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www.mta.info/mta/airtrain.htm»
www.panynj.gov/airports/ ··· ain.html