Via RV, you could move between a few spots.
Mission Bay is by far a more beautiful area to sail and easier access to the Ocean. Lots of area to sail. More protected. Camping is at Campland By The Bay.
http://www.campland.com/ Easy trailer launching and free parking at a bunch of spots around the bay.
South San Diego Bay is very industrial on the eastern shore north of the Chula Vista Marina. Lots of ship yards. Tons of open water though. Sailing up into the bay is nice though and around down town under the Coronado bridge.
I would spend my time in Mission Bay if I had the choice. Lots more to do in the area too.