Depends how you plan to get from the airport into the city.
By taxi it doesn't make much difference, although JFK is usually slightly cheaper (is this simething to do with EWR being out of state? I don't know).
Ditto for the minibus shuttle services - doesn't make a lot of difference.
If going via train I agree that EWR is probably the easiest. You can get the subway from JFK but it means a bus transfer.