www.easternstate.org
This is the only place I can think of which MIGHT be willing to accomodate a Boy Scout troop camping out. It’s certainly worth an inquiry to them.
The only reason I’m thinking they might be willing to make an exception is because it is an official Historical Landmark. They do various educational programs all year long and would definitely fit in with your purpose for the trip.
If the overnight stay request is denied you could also look into the hosteling organizations for overnight sleeping and go to the prison for the tours and programs there during the day.
Public Trans. is plentiful in Philly and the prison is just a short bus ride away.
I know that AYH has a really nice spacious house up in Chamounix Mansion in Fairmount Park which accomodates groups and the rates are really reasonable compared to hotels or motels or something and the Scouts would enjoy the grounds there.
If you go during the month of October, there is also the Terror Behind The Walls tour at night which is like a haunted house type of program.
But they do have regular educational programs all year long and I’m sure would welcome a Scout troop.
www.hiusa.org
This lists the locations and pertinent info for hostels. You don’t need to make reservations through the main site but can contact each property individually. I’ve stayed at the one in Fairmount park several years ago. Spacious building and property and cool friendly staff.