You can take the PATH train, it drops you off at the World Trade Center site. I think it costs $1.35. The PATH departs from Newark Penn Station, so you have to take a bus from the airport to get there..but I can't remember exactly which bus it is, maybe the 60??

Go to an information desk at the airport and they'll be able to let you know. The bus fare is like $1.50.

You can also take the NJ Transit which goes from Newark Penn station to NY Penn Station, but that's like $15 each way.