I live in South Jersey, and the only place anywhere in the area that I know of for sure, where you can live aboard a houseboat, is Sea Village on the Margate Bridge Causeway, outside of Atlantic City.  And yes, you're right, it's a little over an hour to get to Phila. from there.  Another place you can check is in the Riverside area in NJ, along the Delaware River.  Check with the different marinas in that area.  A while back ('70's or '80's), I knew two different people who lived on houseboats along there but I can't remember the name of the marina.  As I recall, it was sort of a ramshackle boat yard.  You never know, it may not even exist any more...  But it wouldn't hurt to take a Saturday or Sunday drive and check out the area.