I dove La Paz last August (and am going back again this Ausgust, yay!) and I can't say enough about the Sea of Cortez. It was 88 degree water and 50-100' viz. We saw Mantas, Whale Sharks, sea lions and snorkeled with wild dolphins. Check out the My Gallery link in my signature if you want lots of pics. We wore 3mm full suits, I recommend some kind of suit as there are little hydra jellies that sting.
I don't know where they will take you diving out of Cabo but I assume it will look fairly similar, Cabo is closer to the Pacific so it might be a bit different. I haven't done the Caribbean yet so I can't compare.
Footslogger: Check out Club Cantamar. They are a resort just outside La Paz and their location saves 30-60 min a day on boat trips; they run their own dive op so it's all in one location and one price and they were great. They also do liveaboards which you can check out.
Can't wait to go back!!!