There are many good small operators that will pick up and drop off who provide personalized service and spacious boats with small groups.
I'd stay away from Red Sail, Foster's, Treasure Island, Sunset for the reasons cited above.
I've had very positive experiences personally with DNS and Wall to Wall. Big boats, small groups, valet service and good DMs, who will guide you if you want or leave you alone after watching your skills on the first dive.
Different posters have other recommendations. Neptunes, Off the Wall, Deep Blue and Living the Dream seem to have good reviews as well, but I have no direct personal experience. Most of these ops will also dive the North Wall as well as the West if conditions permit. Wall to Wall also occasionally does a 3 tanker heading down to Babylon for the first dive. Worth doing if they are going and you have time.
Where are you staying? The shore diving at Turtle Reef and Lighthouse is easy entry, calm, and pretty good as well.