To be honest I was very underwhelmed by the diving in Cabo San Lucas. I've also been to Cozumel and thought that was 100x better than Cabo San Lucas which was crowded and didn't have much life around corals by comparison. We dove there for 4-5 days in December when it was quite cold - we were prepared for cold water but topside was unusually cold <20C, so that didn't help the experience. One bonus that time of year was that from the boat we saw several whales breaching in the distance and could occasionally hear them underwater. We were also unlucky and had bad visibility and didn't see anything big - I understand it can be pretty amazing if you go the right time of year and get lucky enough to see schools of rays, sharks, etc. But for us - combining the cold, bad visibility, not a lot of life among the corals AND not seeing any larger life - it was underwhelming and expensive for the experience. Topside, the scenery is beautiful and our favourite part of the whole trip was driving through the desert and mountains. That and the food - we avoided the mainstream restaurants. Of course there are a lot of touristy things in Cabo San Lucas, they are just not our style and we much prefer the laid back and local vibes of Cozumel.
We also went to Cabo Pulmo and La Paz. Cabo Pulmo I think could be very nice but for us, again the visibility was too poor to tell. La Paz was extremely disappointing after everything I had read - we went to the closer sea lion colony and not one sea lion came underwater during our dive. Particularly bad because the dive shop (Phocea Mexico) had set very high expectations before we left saying "diving with sea lions is guaranteed". I understand that the dive shop has no control over whether sea lions decide to swim while we are diving, but perhaps they should consider not making those kind of "guarantee" claims and temper their customers' expectations to avoid massive disappointment. Then, we were signed up to snorkel with the whale sharks through the same dive shop but apparently the company Phocea contracts with did not properly sign up for the queue to enter the bay where the whale sharks are, so we waited around for an hour and then were told it wasn't going to happen. Super disappointing since that was a simple logistical thing both Phocea and the company they contract with should have been aware of and could have addressed. We were only there for a day and were very sad to have missed both sea lions and whale sharks. Hopefully Phocea Mexico has sorted out their logistics so they avoid disappointing people. (I should say that as a dive shop Phocea Mexico runs a good operation - new equipment, new boat, fun dive guides, attention to safety - no complaints there.)
As for dive shops in Cabo, I researched several and all of the main ones seem like professional and well-run operations and have positive feedback on this forum as well - Dive Nautilus, Manta Scuba, Dive Cabo, Dive Ninja - doubt you can go wrong in that regard. Happy diving and hope you have better fortune than we did!
