The cheapest bus option is the Chinatown bus!
http://www.ivymedia.com/
If you are taking SEPTA you have to take R7 line to Trenton and change over to the NJtransit Northeast Corridor Line ( NEC) to NY Penn Station.
Amtrak will cost you 3-4 times the SEPTA/NJ Transit fare. If it is on time, it may be less painful than the SEPTA/NJT option.
Good Luck and enjoy both the cities.