Sorry I didn´t respond to this before, I was having trouble logging in. Yes, I think you´d be much happier on the Baja side, particularly in the southern tip. (Although Divers Mulege has quite a nice scuba operation, and might take you free-diving as well)
Cabo San Lucas offers clean, clear water, and some cool shoreline out along the Capes (towards the famous arch). There are also deeps there--ask local dive shops about the Sand Waterfall to see if it is in your depth range. This amazing cataract of sand was explored by Jacques Cousteau.
There are other dive sites along the "corridor" to San Jose del Cabo. On the East Cape, near Frailes/Cabo Pulmo is the only Coral Reef in Baja, maybe the only one at such a high lattitude in the world--lies near shore, depths of 30-100 feet as I recall.
Your best bet might be boats out of La Paz. They go out to the Islas--Espiritu Santu and Partida--which are unihabited, leading to pristine conditions, colonies of sea lions, etc. Also out in that area is a unique location, El Bajo--The Seamount.
This is an incredible area where giant manta rays school and have no shyness about divers, allowing themselves to be touched and ridden (most photos of people riding mantas probably come from here). It´s considered a scuba site because of the depth, which I think is around 100 feet to 40 meters but could be wrong. If you can do that depth, it could be the rush of a lifetime. Check with local tour services.