Thanks guys - I was perplexed myself and the only thing I could think was that the direct lines are already sold out. I'll try the Megabus as I've only tried Greyhound and Boltbus so far.

You can check Greyhound here:

http://www.greyhound.com/home/

There are even Chinatown buses. Seriously, there are many buses that take you between Philly and NYC within two hours.