There is indoor parking right at the pier. Drop your luggage at the curb and follow the arrows to the parking garage. A bus will pick you up right in the garage and take you back to the pier. It's a short distance and also easy to walk if you wanted. I don't know what the cost is but my recollection is that it was reasonable.
We live in Phila. There is a parking garage; it purports to allow only 7 day maximum parking, but firends of ours did a post cruise package and made arranagements for 10 days. The port has a web site -- http://www.cruisephilly.com/directions/driving/