Spa Creek (1st creek south w/bridge) - has a couple mooring fields .. right past the Eastport bridge as well as further back. If you continue back, there are several areas to anchor including outside Truxton park. Water taxi service is avail, but also recommend a dink. Any place a public road ends at the water is an open place to land/tie a dink. If you look at this link, you'll see all the roads ending on the shore of Spa Creek (like Conduit St or Burnside St)
Back Creek (next creek south) - several places to anchor .. closer to Eastport destinations, further from Annapolis destinations
In front of the Naval Acedemy is an anchorage .. but it's not protected and can have quite a bit of traffic and choppy.