However, on the mainland side, from Paya Del Carmen down all the way to Tulum (the only Maya ruin by the sea), there is very little damage as Cozumel being a barrier reef and took the blunt.
You may want to do some research on diving operators in places like Akumal, Costa Maya, or just a generic name "Maya Riveria". You will find a lot of operators in that area. I believe the visibility there would be better than those in Pueto Rico. Costs may also be cheaper too.
Bahamas are also very good. Ditto Cayman Islands but Cayman is much more expensive than Mexico or Bahamas.