Ok, here is the deal. I have only taken that route twice. One by Amtrek, which is a total rip-off, the other by Chinatown bus.
Chinatown bus is the CHEAPEST WAY! It used to be $10 roundtrip but they just raised it to $20 round trip in the beginning of Dec (I am still pissed off about that).
Bus can be taken in New York. The previous poster is correct. Take it at 88 East Broadway (and that's in NY chinatown). It is right underneath the Manhattan bridge, I believe. Phone number 212-227-5024. When finding that on the map, be careful: there is a big, huge, famous street called Broadway and there is another smaller street call East Broadway. They are different. East Broadway is not simply Broadway on the east side of Manhattan. Both streets can be found in Chinatown, so don't get misled like me who just kept on following the big famous Broadway for 10 minutes without seeing East Broadway labeled anywhere close to it.
The bus will take you to 1041 Race st in Philly Chinatown (between 10th and 11th st). the phone number there is 215-351-9168 or 215-351-9167. Philly chinatown is within center city. Depending where you will get interviews at. It is within walking distance from Thomas Jefferson (10 minutes at most). However, you need to take public transit if you are going to Penn or Drexel/MCP.
The buses come and leave about once every two hours. Call for exact time. I personally find it convenient because you can grab cheap food in Chinatown when you leave and arrive.