A few years back they built an AirTrain that runs from the terminals at JFK to Jamaica Station (LIRR) and the subway. So much better than the old A train to Howard Beach and the 1/2 hour bus ride to the terminals.
Of the two, I'd choose Newark. Faster to lower Manhattan by cab / uber-lyft or by train. You can take the Airtrain from the terminals to the NJT/Amtrak station, then either ride to Penn Station in midtown or get off in Newark and take the Path to lower Manhattan.
I do American into JFK, then the Air Train up to Sutphin and E line into Manhattan, should be a stop relatively close to where you need to be You can also do the LIRR into Union Station from there It’s relatively painless, Subway sucks with luggage but you can deal with it
i've got a full day layover in JFK end of next month and want to meet some friends in Manhattan for a few hours. are there lockers or anyplace to store luggage at JFK to avoid having to haul it around on the subways? i lived in Jerz for awhile, so i'm at least comfortable with the mass transit part...
I remember having to catch a damn city bus the last time I tried to take a train/subway into Manhattan. That might have been the time I pretty much decided I was never going back to JFK. One too many lousy experiences. I switched to Newark until I moved out of the area.
For me, the train from DC to NYC is easier. I gave up trying to fly there. If I had to choose I'd go Newark. It's old, dark and smells like a NYC peep show but it's less of a hassle than JFK.