My favorite dive spot in Baja is El Bajo or Las Animas, one is a sea mount the other a small rock island.
The dive sites can be gotten to from La Paz or Loreto. Baja Outpost is a great dive oriented motel/dive boat operation in Loreto.
Most people aren't aware that the Sea Of Cortez is claimed to be among the most bio-diverse waters in the world.
In dive spots further south in the sea you'll see a mix of eastern pacific fishes and Indio-Pacific fishes- all at the same time.
There are mantas, scalloped hammerheads, whale sharks, blue whale, and numerous other sitings of "big stuff" depending on the time of the year.
Diving in the mid-riff islands is fantastic, but you'll need your own source for air fills. There have been compressor operators working off and on over the years in Bahia De Los Angeles. So you chould check some web sites before heading there.
The further south in the Sea of Cortez the better it gets. Cabo is unimpressive in my experience and more expensive than La Paz or Loreto.
Don't expect the same level of "resort style" diving you'd find else where in the world. It's rustic, but a great adventure.
shep