We haven't toured Baja in an RV or with an RV tour company, but since no one has responded to you yet I'll jump in with some thoughts.
We toured the Sea of Cortez on a sailboat for two seasons and spent a lot of time in the Bahia Concepcion area (Coyote Bay, El Burro Cove and Isla Requeson). The RV park in Coyote Bay looked wonderful but was empty when we were there (May and October -- too hot). The boondocking at Isla Requeson looked awesome as it is right on the beach.
(We have also explored mainland Mexico RV parks both south of Puerto Vallarta and near Mazatlan, and they were lightly inhabited, very cheap and on the beach...!!)
If you are thinking about a tour company because of safety, I'll just say that we've been in Mexico on our boat for 2+ years and have felt very safe everywhere along the entire coast, especially in Baja. We leave our dinghy with outboard attached on the beach without worrying about it being stolen. So I would imagine that venturing there in an RV would be similar -- all the RVers we have met in Mexico are loving there time there and have had the same experience of feeling very safe and unthreatened.
The only negative I have ever heard about RVing in Mexico -- and I've experienced it myself in public buses and vans -- is the preponderance of very tall speed bumps on the highways.
There are two websites I've watched for a while that talk about RVing in Mexico (you may know these already) -- On the Road in MexicoA Comprehensive Travel Guide to Safe Driving, Camping and RVing in Mexico
and Rolling Homes Press
One or both of these resources might help you locate a tour company or give you the confidence to venture there on your own.
Good luck and buen viaje!