I live in the area (1/2 hour to the south) and will give you the best overview I can. Most of the friends I ride with live in Annapolis so I trailer up to them most of the time.
To my knowledge there isn't much of an organized "scene" right in annapolis, you will see riders out on the water but I don't know of any network of riders that really exists. It's very possible that I'm wrong about this and I'm just an outsider but that is as much as I know. The closest boardshop is Skihaus off of route 50, there is probably a group of riders associated with them and could point you in the right direction. In DC there is a more organized "scene" centered around www.dcwake.com
these guys mostly ride on the Potomac river and Lake Anna in Virgina, some also ride in southern Md on the Patuxent river.
Annapolis is a really big boating community so the waters are always busy with sailboats, cruisers, fishing boats and whatnot. You will see people out wakeboarding and skiing behind whatever they have like fishing boats, jetboats, and runabouts but there are few full on wakeboard boats in the area. There is limited protected water and much of that is restricted by no-wake zones. Weekends on the water in Annapolis can be a total cluster. People ride at the north end of the Severn River and any other place along the river they can find some sheltered water but this can be a really high traffic river on the weekends. If you can get out on weeknights or early on weekends it is much better like the difference between night and day.
Just south of town is the South River (imagine that) which I have no experience with at all because the only public ramp on it is $20 and it is not worth putting in elsewhere and running over to.
Further south of annapolis is the west and rhode rivers. The head of the rhode river is my preferred spot to ski in the area especially in the evenings. There is more protected water, and while it is heavily it is less hectic than the Severn in my opinion.
Further south is the Patuxent which offers lots of protected ridable water and doesn't get much traffic at the northern end. The problem is a lack of public ramps.
North of Annapolis is the Magothy which has some nice areas to ride but that is about an hour drive from me so I never ride there.