I hope my post isn't too late.
I live in aguada, about 5 minutes from downtown Rincon. This is the north-western tip of the island. This place is a world-class, world-famous surfspot, but in the summer it is flat and calm. To be clear, it is the reef here that helps to make the surfing so great in the winter. I had no idea what I was surfing on top of this winter until I took a look below the surface this summer.
The major chartered dive spot is desecheo island, which you can see clearly from most beaches on this end of the island. If you are interested in underwater topography and neat coral formations, you will love these dives. The major charter here is an outfit called "Taino Divers", and they are located right off of the famous 413 surf strip. This is, so far, the best openwater diving spot that I have found off of the main island.
There are also two places here where I like to snorkel in the summer. Steps Beach (Escalares), which is the main access to a small marine reserve known as Tres Palmas. About 3 - 4 times a winter, Tres Palmas becomes one of the best surf spots in the world. It is a stone's throw away from Taino Divers in Rincon. If you charter with them, they'll be able to tell you all about it. This place is a forest of elkhorn coral, sea fans, and there is a LOT of fish life here. Much more so than anywhere else I have been in Puerto Rico. I always see schools of squid (even in the daytime), several tortuga, and most of the normal Caribbean fish sights. No tank is necessary here, but it would be nice for a free beach dive if you wanted a closer look into the slightly deeper reef walls. If you are not content to have just 2 desecheo dives in one day, you can head right up to Steps Beach to get in some snorkeling before the day ends.
A second place where I like to snorkel is a place called Shacks Beach. Shacks beach is a world class windsurfing and kitesurfing spot and is featured in many magazines. It is located on the opposite side of Aguadilla on the line between Aguadilla and Isabela. It is about a 20 minute drive from my house. There is a hole there that is like a maze. It becomes so shallow in spots that you have to plan your route to get through it. At other places it goes down into 15 - 20 ft deep systems of holes and swimthroughs. There are 100 yards or so of interconnected caves and TeePee's created by the coral. I swim through many of them by holding my breath, but there is a lot more to explore if you have a tank. There is a respectable amount of sealife and coral here, but the overall topography of this little spot makes it really special.
Both of these are great spots because they are free. If you have your equipment, it will only cost you a tank's rental if you prefer to have air. Both of them are pretty spectacular, even more so considering that they are beach dives.
The other famous spot here on the main island is La Parguera, down in Lajas. The water there is arguably the most beautiful on the main island and the reef is everywhere. Unfortunately, my dad and I were sorely disappointed when we dove there. It was much prettier on the surface, than on the ocean bottom. One of my close neighbors has a weekend spot there and he agrees that it is better for boating, windsurfing, and kayaking than for diving and snorkeling. The most unique thing here is that you see large quantities of black coral, which is much less impressive alive than polished and made into jewelry (not that I am condoning this ... just trying to make a point). Many people post that it is a great spot, but I have yet to be impressed.
I started learning to dive out in the Florida Keys. In the keys, every reef is teeming with large quantities of every type of fish that you would expect to see in the Caribbean. Sea Life is everywhere. When you dive in Puerto Rico, you will see plenty of reef and some very unique coral formations, but you will probably notice that there are not many fish. One of the quirks of the island I guess.
Some other tips in general about Puerto Rico: We are located very close to the equator, and so the sun hits you at a very direct angle. If you have irish in your blood like me, you can be sunburned in less than 12 minutes. Even the dark-skinned locals wear sunscreen here. Also, the rock-bottomed beaches are littered with small urchin in every little crack. Be mindful of where you step while in shallow water.
Let me know if you have any specific questions. I've lived here on the island for just over a year and I am still learning about new spots myself. If you can grab an avid local, you will find worthwhile diving all up and down the coast of Porta del Sol. There are random reefs that not many people know about. I am hoping to see Vieques and Culebra before the summer is over.