It's not hard to find a great spot to go snorkelling. Every coast on the island, along with all its adjacent islands, to say nothing of Vieques and Culebra, offer excellent opportunities to view marine life. My personal favorite is to combine a day of snorkeling with a day out on a boat. From Fajardo you can charter a number of boats that will take you to the islands around mainland Puerto Rico and drop anchor at least twice so that you can jump into temperate waters and see what there is to see.
Two such operators are Erin Go Bragh and Ventajero.