The AirTrain doesn't go to Penn Station. It's just a shuttle that takes you from JFK to the nearest subway stations (the Howard Beach Station on the A train, and the Sutphin Boulevard-Archer Avenue station on the E train and the J-Z line).The Howard Beach station is much closer to JFK (you'd only go to the Sutphin-Archer station if you need to take the E or J-Z). You can take the A train to Penn Station, so get off the AirTrain at the Howard Beach station.Then take the Manhattan-bound A train from Howard Beach to 34th Street-Penn Station. The ride on the A train is about an hour to an hour and fifteen minutes. The AirTrain takes about ten minutes. So you're looking at about an hour and a half trip from the airport to Penn Station.
At JFK, you can get a shuttle (called the AirTrain) from inside the JFK terminals to the Howard Beach Station of the A train (on the A-C-E, which is the blue line). The A will take you to Penn Station (34th Street). From Penn Station, you can take the LIRR (Long Island Railroad) to either East Hampton, Westhampton, or Southampton. I have included a link to the LIRR home page where you can get the schedules.
The closest subway stop is the Howard Beach Station on the A train (of the A-C-E, the blue line). You can take the shuttle, called the AirTrain, from inside the JFK terminals to the Howard Beach Station.You can also take the AirTrain to the Sutphin Boulevard-Archer Avenue Station on the E train and the J-Z (the brown line). But the AirTrain ride from JFK to the Sutphin Boulevard-Archer Avenue Station is almost 4 times as long as the ride from JFK to the Howard Beach Station.
Penn Station.
Yellow cabs charge a flat rate of $45 (NOT including tolls, tips and tax) for all trips between JFK and Manhattan. Car service companies will charge similar rates. By train, it will cost $7.50: $5 for the AirTrain shuttle from JFK to the Howard Beach subway station (on the A train, of the A-C-E, the blue line), and then $2.50 for a Single Ride subway ticket. The A train stops at 34th Street-Penn Station in Manhattan.
If you don't want to take a taxi, you can take the subway, which costs only $2.25 to date (October 9, 2009), plus the $5 you will need for the shuttle. The shuttle (called the AirTrain) takes you from inside the JFK terminals to the Howard Beach Station of the A train (on the blue line). You can take the A train straight to Penn Station.
From JFK you can take the air-tram to the Howard Beach/JFK airport stop on the A subway line. That is an express train that goes to 34th street-penn station. Getting off at this stop puts you directly in Penn Station, all you have to do is follow the signs. If you are coming from Penn Station going to JFK airport, make sure to get a on JFK/Far Rockaway bound A train, there are 3 different A trains.
From JFK, take the "Air Train" to Jamaica Station. There, you can catch the LIRR (Long Island Railroad) into Penn Station in Manhattan. From Penn Station, you can catch an Amtrak train upstate to Albany.
There is a $45 flat rate for yellow taxis (NOT including tips and tolls), for all trips between JFK and Manhattan. Car services such as Carmel (212-666-6666) or Dial 7 Car & Limo (212-777-7777) charge similar rates (between $40 and $50, again, NOT including tips and tolls). Yellow cabs carry up to four passengers, and car services likely have the same policy. If you take Super Shuttle (1-800-BLUE-VAN) it will cost $26 for one passenger to go from Penn Station to JFK, and $37 for two passengers. For each additional passenger, the per-passenger charge is cheaper. You can also take the subway, for a total cost of $7.25 ($2.25 for the subway, and $5 for the shuttle, called the AirTrain, to the JFK terminals). Take the Downtown A train from 34th Street-Penn Station to the Howard Beach Station. At the Howard Beach Station, get the AirTrain to the JFK terminals.
It's the Downtown A. The Howard Beach station (where you transfer to the AirTrain shuttle to the JFK terminals) is near the Downtown end of the A line.
You can get from JFK to Penn Station by subway: you take the shuttle, called the AirTrain, from inside the JFK terminals to the Howard Beach Station of the A train (of the A-C-E, the blue line). The A train stops at Penn Station. Very few subway stations are accessible by wheelchair. Penn Station is one of the few that has elevators for wheelchair patrons, and the shuttle (the AirTrain) is also wheelchair accessible. The Howard Beach Station is wheelchair accessible, too. So you are in luck. See the Related Links below for more information about wheelchair access and public transportation in New York City. If you want, you can also just take a cab. You can always get a yellow cab at the airport, although you might have to wait awhile for one. If you don't want to wait, you can call a car service in advance to pick you up. There are two main car service companies that service the New York area: Carmel (212-666-6666) and Dial 7 Car & Limo (212-777-7777). Both provide excellent service; it really doesn't matter which one you pick.
Take the Downtown A train (of the A-C-E, the blue line) from 34th Street-Penn Station to the Howard Beach Station in Queens.At the Howard Beach Station, get the AirTrain shuttle (for $5), which will take you inside the JFK terminals.