Getting into the New York City area can be a nightmare.  There are many airports to fly into but getting between cities is relatively easy by trains.  I have combined the New York City guide and the Philadelphia guide as the truly adventurous traveler would be willing to travel between the two major metro areas to save a few bucks or to just see something new. 

Below is information on how to get to each clinic by Amtrak (if available), regional train, regional bus and local bus/transit. 

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Airports:	LaGuardia Airport (LGA) Newark Liberty International Airport (EWR) John F. Kennedy International Airport (JFK) Long Island MacArthur Airport (ISP) Islip/Long Island Philadelphia International Airport (PHL)
Airport Transportation:	Getting to Manhattan; Penn Stationor Grand Central Terminal.    For JFK, LGA and EWR: click here.   For Long Island MacArthur Airport (ISP): There is shuttle service from MacArthur Airport to the nearby Ronkonkoma train station: Colonial Transportation of Long Island offers convenient shuttle service between MacArthur Airport and the Ronkonkoma train station (LIRR). The shuttle van departs the train station daily at 5:30am, then departs the airport on the hour and half-hour from 6:00am until 10:30pm. Curbside pick up at the airport is directly in front of baggage claim. The shuttle will pick up and drop off at the North Platform of the Ronkonkoma train station. The one-way fare is $5.00 per person. Cash and credit cards are accepted.   The Suffolk County Bus Transit also offers hourly service to and from MacArthur Airport to the train station with the S-57 Bus except Sundays and holidays.   The Long Island Rail Road (LIRR) offers frequent service to Penn Station in Manhattan from the Ronkonkoma train station The train ride is approximately one hour and 25 minutes.  The train fare currently $9.75 (non-rush hour times) into the city will take you to Penn station which is located in Manhattan at 33rd street and 7th Avenue.   I have gone this route before and it wasn't too bad.  Flew in on a cheap Southwest flight and traveled into Penn Station.    For Philadelphia International Airport: You must first take the Septa train R1 to 30th Street Station.  Take the R7 to Trenton Transit Center.  Then take the NJTransit - Northeast Corridor (pdf) to NY Penn station.  Total cost about $20 each way.  Amtrak - There is plenty of service between Philadelphia and New York City.  Regional service is your cheapest option and takes about 1 hour and half to 2 hours depending on time of day.  Acela Express offers quicker service, just over 1 hour but at a steeper price.
Regional Bus:	Port Authority Bus Terminal (Wiki) 625 8th Ave The PABT is the main hub for Greyhound buses as well as regional buses serving PA, CT, NJ and more.   Here is a list of bus carriers that serve the PABT Several MTA subways stop at Penn Station.  A, C, E, N, Q, R, S, W, 1, 2, 3, 7, 9 drop within 2 blocks.   Greyhound Bus Junction Books Most East Coast Bus Travel including Greyhound and Megabus   Megabus also provides service between New York City, Philadelphia and Baltimore as well as other major points on the coast.  Megabus is famous for have seats as low as a dollar plus reservation fee if you book far enough ahead.  All online reservations.
Trains:	A general rule for all trains especially regional and local transit is that you must buy your ticket in advance for cheapest fare.  This can be done at the departing station from an agent and or from a vending machine.  You can buy your ticket on board but you will pay a penalty if there was a ticket agent or vending machine at the station you boarded from.    Pennsylvania Station (Penn for short) (Wiki) 7th Ave between W 31st St and W 33rd St MTA subway routes 1, 2, 3, A, C, and E.   Amtrak (Amtrak - Penn Station) - All Amtrak trains come into Penn Station.     New Jersey Transit - Some leave from New York Penn Station while the rest can be connected at the Secaucus Junction station.   Long Island Rail Road (LIRR) - 'Ronkonkoma' line connects to Long Island Islip Airport.  (More info)   Grand Central Terminal (Wiki) 15 Vanderbilt Ave MTA subway routes 4, 5, 6d, 7, 7d and S.    Metro North Railroad - 'New Haven' line provides service to Pfizer New Haven Clinic.   (800) 872-7245 Amtrak (800) 772-2222 NJ Transit 24 hours (800) 638-7646 Metro North Railroad (718) 217-5477 Long Island Railroad
Subway: Local Bus:	MTA provides subways all over the boroughs of New York.  MTA provides bus service throughout the boroughs of New York. To ride the subways or buses, you need a MetroCard.  Most stations have automated vending machines to purchase and reload cards. The one-way fare is $2 You can also buy passes.  A 24 hour pass is $7.50 and a 7 day pass is $25.  These can also be bought a vending machine. Ask any station attendant for a free subway map. (718) 330-1234 MTA Info
Taxi:	The familiar Yellow Cabs of New York are the only cabs allowed to pick up passengers via "street hail".  All other cabs are known as "gypsy" cabs.  Only take a Yellow Cab.
Hostels:	There are many hostels in New York.  Check out this website for a list of them.  Here are a few I'd recommend.  Hostelling International New York   (212) 932-2300 - 891 Amsterdam Ave A tad bit on the pricey side compared to other hostels in the area but I go there because it's part of a chain of great hostels.  Big Apple Hostel   (212) 302-2603 - 119 West 45th St