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I've been to both Cabo and Coz, as cruise stop, for diving/snorkeling. In Cabo, most of the sites are not far from each other, and not far from the dock. They are fine, but nothing spectacular. The water is colder, and coral growth ok.
Cozumel is a different story. Coz had 130+ dive shops, most are very good. Lots of resorts/hotels that cater to divers. There are lots of world class sites. Coz constantly gets ranked among the top diving location in the world.
I've made week long trips to both. Dive in Cozumel, fish in Cabo. Cozumel is much less expensive, at least the way I did the two. Both are great destinations, but are polar opposites in what they offer, IMO.
In Cabo, there's a good chance to see sea lions, and rays. The water is colder, even in mid summer. Viz is not as good. 50' is not bad. Not many ops have larger tanks. Cabo is a popular resort destination. Not much else nearby. You'll quickly cover most of the dive sites in a few days.
In Cozumel, viz is often >100'. Water is warmer. The continuing flow of water bring nutrient to the corals, and fish. It's drift diving. As such you can dive effortlessly if you just drift along and can cover some distance in a dive. There are so many good dive sites. There're lots of amazing coral formations. You can spend weeks and still not cover many sites.
Also in Coz it is very easy to get larger tanks, many shops have 100s, and enough shops even have 120s. Coz is a very popular diving destination, but also enough not-just-diving resorts. Coz has some ruins to see, and just across the sea from PDC, other ruins, cenote diving, and not far from Cancun.
My wife and I took our first trip to Cozumel last November (09) and stayed at Occidental Grand, all-inclusive. We simply LOVED it.
A few things to consider. If you want to be close to town, this is not the place since it's way South. However, we aren't really into doing all the typical MX shopping (etc.) and just like to relax, dive, and relax! But the best part for us was it's AI and was literally 5 minute boat ride to most of the great dive sites. Onsite dive op dive palancar was pretty good once you got used to how they operated. At first we were sort of put off by lack of attentiveness when we first started diving with them. But it was truly so easy and convenient once we got used to it. We purchased their 10 dive package for $300 and split the dives between us. Yes, we only dove 5 times each all week but maybe will do more next time. Like I said, we like to relax a lot also!
Most of their boats are larger and some would consider them cattle boats I guess but personally, I like the larger boats. It seemed as if most people diving there had been there many times and so that says something. Some of the DM's had a little to be desired and at times were the first ones out of the water... George WAS great however. We're already looking forward to our next trip there. The Occidental is a little more expensive then the in-town hotels but we like the fact that it is AI and has a nice beach and very relaxing. Even though it's an AI, it feels small and intimate and not like the bigger AI's we've been to.
We got a great price through Orbitz but having trouble finding a cheap deal to Occidental Grand again. May look at Hotel Coz or something. I really like staying on the South end to keep boat rides short as I'm not a big fan of long boat rides.
Hope this helps, good luck and make sure you stop back here to let us know how your trip goes!
Cozumel is awesome, truely a must see destination. Cabo San Lucas is not that great for diving but La Paz and Cabo Pulmo are the must see spots for Southern Baja. It is totally different diving from Cozumel though. Cozumel is beautiful coral reefs and at La Paz there are excellent big animal experiences and really cool wrecks both natural and artificial. I have been to Cozumel 5 times and La Paz 7 times, I have never seen anything in Cozumal larger than a large grouper and an eagle ray. In La Paz I dove with sperm whales, dolfins, giant manta rays, mobulas, hammerhead sharks very large sea lions (and baby sea lions too) and even an elephant seal to name a few. The schools of game fish are amazing too in La Paz and Cabo pulmo as well. Since you are on the west coast I would say do La Paz. You can rent a car and take 2 or 3 days and drive down to Cabo Pulmo, I think it took me about 5 or 6 hours when I did that if my memory serves me well, but I was not in a big hurry to get there, I wanted to take in the scenery.
Cancun/Cozumel was my very first diving...awesome! Now, first time to Cabo (since I was about 9 anyway) coming up in a couple of weeks. 'Looks like I'll need something warm to wear (5mm) or could I manage a 3mm on a shallow dive? I can't rent anything that would fit there (need 4x to 5x), so I'm trying to plan what to bring. I'm thinking that my 7mm California wear might be a bit too much. Thoughts?