We haven't actually ever anchored in there... primarily only 'cause it doesn't seem to be within walking distance of much of anything. We have friends who raft up there often, though, and they do like it. Ooopps. Wait, I was thinking of College Creek....
But still, we haven't anchored in Whitehall Bay. Did go up to Cantler's a few times, not recently.
For marina stops on this side: Chesapeake Beach is OK. Some folks like Herrington Harbor South at the bottom of Herring Bay, we prefer HH North in Deale and there are other Deale options. Galesville. Annapolis (main harbor or Back Creek). Some in Bodkin Creek, Rock Creek... and Bal'mer. Plus Havre d'Grace if you get you that far. I've heard Middle River has options, too, but haven't been in there...
For anchorages: several options on the West and Rhode Rivers, South River, Severn, Magothy... and almost anywhere with "Creek" in the name.
If you haven't seen it, "Cruising the Chesapeake, a Gunkholer's Guide" by Bill Shellenberger is still a very viable resource for that. A long time ago we anchored in Sillery Bay on the Magothy, often just in the bight above Gibson Island called Eagle Cove I think. 'twas nice then, but it's been a good 25 years or so...
-Chris