I strongly recommend Dive Connections (
www.gottadive.com). They have two boats, cancel less often than any other operation in the city, great captains and really know the spots.
They do three specialties that I recommend you consider.
1. Wreck Alley - I don't realy like the wrecks but they are something you should see at least once. Everyone seems to have heard of the Yukon.
2. Los Coronados Islands.. this is a 75 minute boatride to the islands off Mexico. Visability is usually around 50-60 feet (compared with 10-30 in SD). These are shallow dives at around 30 - 55 feet but the fish are abundant and camera opportunities abound. It is truely delightful.
3. (My Favorite) Kelp Beds. I hunt here, and gather (fish, scallops,crab etc...) but even if you aren't a hunter, it is a wonderful experience. Nowhere are the kelp beds so full of life and mystery. After Oct. 1, this is where we hunt the lobsters.
If you come down and dive after Oct 1, we can go lobstering, bring back any bugs to my place, cook them up, bbq some steaks and enjoy! My husband isn't a diver at all but he does a mean bbq. Hope to hear from you again.