I recommend
Xibalba Dive Center in Tulum. They are a great dive shop, mellow, attentive to your needs and safe. They also coordinate the Qintana Roo Speleological Survey that is discovering new cave routes.
Given that Abyss never showed up at their shoip for our dives and left us to find another dive operator, I warn folks about them.
As far as cenotes are concerned Dos Ojos is nice but can get crowded. There are "out of the way" tunnels so make sure your guide knows them or start the tour in the opposite direction from the traffic. There is not much stilt in Dos Ojos. When you spot the crocodile eating the barbie, you are at the end of the line that was filmed in the 2002 IMAX film, 'Journey Into Amazing Caves.'
If you want to experience diving through a layer of hydrogen sulfide between fresh and salt water then dive Angelita. The dive is otherwise not interesting and it is deep (40m). It is a must-do-once experience.
A great way to experience the fresh/salt water halocline without hydrogene sulfide and a big 3m jump with all equipment into a cave is Temple of Doom. It requires good buoyancy control and gives you a good impression of being into a cave (no light) although it is still technically a cavern dive.
I like Aktum Ha (Carwash) best because you not only have fresh water biodiversity to see but the light effects when you look out of the cave are spectacular. Entry is easy.
Good luck with your trip,
JL