Mick's Scuba is the sole dive shop in Rapid City (or western SD) and one of only 4 in the state.
http://www.micksscubacenter.com/
It's under new ownership and the website should be improving shortly. The new owners (Scott and Tammy) are also talking about expanding the training and dive travel options.
Pactola Lake offers the best overall diving although the water level is down 30 ft due in part to 6 years of drought, but mostly to city water managers and council members that have no concept of how to conserve a natural resource, but who instead prefer to make about 2 million per year selling water from the lake despite a lack of adequate winter snowfall to refill it.)
The result is the max depth is now down to about 110-120 ft and the visibility is reduced from the normal 20-30 ft due to silt being disturbed by wave action to more like 5-15 ft.
The lake starts warming up and becoming 7mm wet suit tolerable in late May to early June with temps from about 60-65 at the surface to upper 30's at 120 ft. By August, water temps peak in the mid to low 70's from 0-30 ft, in the 60's from 30 to about 50 ft and decrease below that to the mid 40's below 100'. The temps hold fairly steady into September and October with the upper 30 feet doing all of the cooling.
Visibility tend to be better in the spring an early summer and also tends to be worse in some of the bays on weekends due to boat wakes and dragging boat anchors.
You can spear bass in the lake, but no other fish.
If you bring your own boat, the north boat launch is still operable and is being extended on a regular basis by the Game, Fish and Parks department. If you do not bring your own boat, Pactola Pines Marina rents pontoons and smaller fishing boats but you'll want to reserve one in advance if you are there in the peak season.
http://www.pactolapines.com/
The former owner of the dive shop still has a boat at the lake and may be available to take you diving. You should still be able to set that up through the shop. I also keep my boat there and would also be willing to take you diving if I am available.
Coldbrook Lake near Hot Springs is another option. It's a fairly small and shallow lake with a 40 ft max depth but visibility tends to be good at 20-30 ft. until late summer when the waater gets excessively warm and triggers an algea bloom. It also gets closed on occassion due to some of the microscopic critters that grow there in the late summer. It's not my favorite lake, but does offer warmer water and good diving in the late spring to early summer.
Cox Lake near Spearfish used to offer a very unique dive. It's spring fed and is essentially shaped like a vase funelling down to a 50' diameter at 65' where you encounter a "bottom" that consists of very liquid sulfferous mud through which the remarkably clear spring water percolates. Temp is about 52 in the winter and 56 in the summer making it an excellent winter dive site. Unfortunately GF&P made the fishing pier handicap accessible and then objected to and removed the gate and ladder needed to access the lake without wading through 50 ft of 2 to 3 feet deep mud. So basically at this point, it's a great dive that we can't access as wading in disturbs mud that then rapidy flows down the sinkhole and destroys the visibility until the volume of silty water is displaced by the spring (a 24 hour or so process).
