Dos Ojos was my favorite cavern tour site, but Grand Cenote is another very beautiful dive, highly decorated. Taj Maha has fabulous halocline effects, including the "Points of Light", if you are there at the right time of day and year. (These are cracks in the ceiling that admit bright beams of light, that hit the halocline and bent sharply. It's very cool.) Chac Mool is a very large room, with a lot of light in it. The cavern dive at Ponderosa (Cenote Eden) is pleasant but is more large chunks of limestone, and not as much of a feeling of being in the overhead. I didn't think the cavern dive at Carwash was all that much fun -- you're really swimming more or less just under the drip line. The cavern dive at Chikin Ha is also more big chunks of limestone.
I'm not sure where else they tend to run tours, but those are the ones I've done.
I'm not sure where else they tend to run tours, but those are the ones I've done.