Copied from my post above.....
I have lived in Puerto Rico for three months and was recently certified here, and while not an expert I do have some good info. In general, the east side of the island near Fajardo, Luquillo and Palmas del mar is characterized by fairly shallow diving (60-70 max with 40-50 being more typical). The visibility varies but gets better the farther off shore you go. This is mainly due to runoff from el Yunque, the rainforest that dominates the north east corner of the island. I have logged roughly fifteen dives in this area, some shore dives and some boat dives in the surrounding cays (small islands) such as cayo diablo and cayo lobos. The shore dives can be quite murky (10-20 foot vis) but once offshore it improves to anywhere from 50-80 foor vis. The reef life is pretty typical if the Caribbean with lots of blue tangs, parrot fish, angel fish, occasional sting rays etc. Though I have not yet been there, many friends of mine who dive say that Vieques and Culebra are quite nice with deeper dives available, better vis and more varied and abundant reef life. Also, it is commonly believed that the best diving on or around Puerto Rico is in the western side of the island near Rincon, Desecheo and Mona. The west side does not suffer from our visibility issues near shore and with the greater depth there are more opportunities to see "the big stuff". Again, I'm no expert but this is what I've seen and heard.
If you do come to the Fajardo area (which has boats that go to Vieques and Culebra on weekends) I recommend diving with Sea Ventures. Their number is 787 863-3483. They are great people and run a good boat. They also have a shop in Culebra, which is supposed to be a nice overnight place to stay if you're interested. If you have more questions drop me an e-mail at erwins@navstarr.navy.mil.
Regards,
Scott