EWR is far easier to get in/out of Manhattan on public transport, the mono-rail drops you from the terminal to the train station - a 20minute train ride for $11 (approx) then takes you into Penn Station - direct/no hassles and no traffic jams - JFK has lots of flights, but depending on the time you arrive/depart it can be a nightmare journey from the city to the airport. (and v.v)