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Isla Holbox isn´t really good for diving (Isla Mujeres is better), but at this time of year, you still have a good chance of swimming with whale sharks, a must do, if you can. Xcalac is a probably the best destination for reef diving and you should try to get out to Banco Chincirro, whilst there. You can get similar diving from Mahahual, which is a little nearer to get to from Highway 307: the road that takes you from Chetumal to Cancun.
Cenotes are a must dive and the three you mentioned are the usual sites we take people to, there are other sites which are just as amazing and have less diver traffic, it depends on your experience level? I am a Cenote guide living and working in the Tulum area, if you would like to discuss organising a possible tour, please feel free to pm me.