We went on an excursion to Rio Secreto during our Oasis of the Seas cruise to Cozumel and it was really amazing. It was about an hour traversing water in a cenote (about a mile and a half). The water wasn’t too deep, but there were several areas that were very, very, very tight. You can read the detailed account here.
The Crystal and Fantasy Caves are very beautiful. We had a great time exploring these caves in a guided tour. You can just do one of the caves if you like, but might as well see both since they are next to each other. We took a public bus, and walked to get there. You can read the detailed account here.