If you're coming back to Manhattan on Sunday evening, do not take the bus! It will take forever. The traffic is horrible. The train will be crowded but your trip time will be the same.

I have taken Amtrak and the NJT/SEPTA trains between NYC and Philadelphia, and I greatly prefer NJT/SEPTA. Amtrak can get just as crowded as NJT, but it stays crowded the whole way, whereas NJT will thin out after a few stops. Amtrak costs three times as much, and when it has the inevitable delay, it's not much faster than NJT.