Not many choices on the Delaware side of the Bay; try Delaware City Marina on the original C&D canal just north of the entrance to the C&D. Delaware City is a very pretty little town.
North of Lewis near Slaughter Beach is Cedar Creek Marina, mostly power boats.
For ammenities Lewis is a great destination, a very attractive historic district and bus service to Rehoboth Beach.
North of the C&D there are no marina's on the Delaware side, until Essington PA. Essington is under the approach to Philadelphia International Airport so the noise makes it less than desirable for liveaboards, but Anchorage Marina does have some liveaboards, and has a strong current, most slip have at least 17 ft water depth at low tide. Also The Lagoon resturant and marina and 3 or 4 other marinas in Essington.
In Philadelphia there are 3 marinas near the Ben Franklin Bridge and walking distance to the historic area, all liveaboard tolerant, try the Philadelphia Marine Center which I think Kernix mentioned, or Dave and Busters Marina.