We lived in the Black Hills for 30 years. Didn't have a C-Dory at the time, but we did occasionally take our sailboat to other lakes in South Dakota. The South Dakota "Great Lakes" (reservoirs along the Missouri River) offer some great boating. Here is a link to ramps and boat access...
http://gfp.sd.gov/fishing-boating/fishing-access.aspx
If you want to stay in the Black HIlls, just south of Hot Springs is Angostura Reservoir; a relatively small lake, but in a beautiful area. You could stay on your boat and day trip out of there with your truck. Mid-week is generally quiet (this holiday week will be an exception). There are places you can beach the boat and have a picnic. We kept a sailboat at a marina there for several years. It is in a state park, fees will apply.
The lakes along the Missouri at MUCH larger (you can be out of sight of land on Lake Oahe); at one time, the SD state tourism board used to advertise that South Dakota has more shoreline along the Missouri than California has along the Pacific. South Dakota - who knew? 8)
The Black Hills area is beautiful; besides the well-known tourist attractions (Mt. Rushmore, Crazy Horse, Badlands, Custer State Park), there are lots of great roads and wonderful natural views. Spearfish Canyon is a gorgeous drive; a walk back to Roughlock Falls will be nice and cool on a warm day. Iron Mountain Road (between Mt. Rushmore and Custer State Park) has a zillion curves - fun on a motorcycle, don't tow your boat through there! You could spend weeks in the Black Hills and barely scratch the surface for all there is to do there.
Most of the water recreation in SD is on reservoirs - and having decent water level is VERY dependent on how much is released for irrigation and how full the reservoirs are to start. Poke around on the SD state site above to get more info.
Have fun!
Best wishes,
Jim B.