Definately Newark or LaGuardia. JFK is the pits. Newark has good busses from the terminals into the City, so you don't have to worry about changing trains etc. If my memory serves me, they have ones that go to both midtown (Port Authority Bus terminal) and lower Manhattan (formerly the WTC, who knows now).

Metrocards are a very good thing, and the subways and busses are easy to use. Quick orienting tip: even numbered streets run east, odd ones run west. Avenues: even go north, odd go south. There are exceptions, but its a good rule of thumb to help you get oriented when you emerge from the subway.

Have fun in the big Apple!