It would be easier to fly into Philadelphia, which has a major international airport.
To get from JFK to Philadelphia you take three trains: first the AirTrain to Jamaica, then the LIRR to Penn Station, and finally the Amtrak to Philadelphia. You never have to actually go outside, but you're lugging your stuff around the three train stations.
Delta has three nonstop flights daily from JFK to PHL as well.
The train would leave from Penn Station in Manhattan so first you would need to make your way in there from JFK
It depends on how big (or difficult to maneuver) your luggage is. If you want to simplify the process a bit, you could get a taxi or car service from JFK to Penn Station and then take Amtrak to Philadelphia. Once you're at Penn Station, you can get a red cap to help you with your luggage.
If I were in your situation, I'd check the cost of an "open jaw" ticket from your point of origin (Honolulu?) to PHL and then JFK back home. It might not cost much more than a round trip to/from JFK.Edited: 09 July 2012, 21:44
It's certainly easiest to fly to Philadelphia. But if you really want to fly to New York, there are two options once you get to Penn Station. You can either take one Amtrak train from New York to Philadelphia, or you can take a New Jersey Transit train to Trenton and then a SEPTA (Philadelphia-area public transit) train to Philadelphia. Amtrak is faster, easier, and nicer. New Jersey Transit and SEPTA are cheaper.
It's not all that hard, if your luggage is manageable.
You'll walk about 5 minutes to the Air Train stop outside your terminal at JFK; then take a 10 min trip to the Jamaica station of LIRR; then walk just a bit, and either take an elevator or escalator down to the tracks for the train to NYC; you will wait 5-15 minutes for that train, then take a 20 minute trip to Penn Station. Total fare will be about $14.
From there, you'll have a very short walk, up an escalator or stair case, to Amtrak. On the other end, you'll be at 30th St. Station in Philly, which is pretty convenient to downtown Philly.
The other option is a cab to Penn Station. It will take 40-75 minutes, and cost about $45.
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