We ended up driving to Staten Island, where we parked at the Staten Island Yankees ballpark. For $7/day, we got a gated lot, with overnight parking privileges, and only a 5 minute walk to the SI ferry terminal.
By driving that far, we got a lot of flexibility in terms of when to leave home/NYC, and avoided dealing with taking the train into downtown Philly - our parking charge was less than RT to downtown would cost.
And why is full-serve gas 40¢/gallon less in NJ than NY or PA self-serve?