I am glad to see this thread.
I grew up in PR and started diving there in 1971. I also started working at Divers Service Center in 1971. This was the only actual dive shop in the San Juan Metropolitan area back then (there were a couple of hotels that had compressors and had some Scuba gear).
I am always happy to see that Alberto is still in business with DSC, but now he caters mostly to local divers. The building looks almost the same as 50 years ago and he still has the same phone number. Look at the link below.
https://www.google.com/maps/uv?pb=!1s0x8c0368e34a2816e5:0x2958cb049e30f1c3!3m1!7e115!4shttps://lh5.googleusercontent.com/p/AF1QipNbbcEcQqSZed2aoJzgqXASU9RDr-FTGKYh0481=w120-h160-k-no!5sdivers service center puerto rico - Google Search!15sCgIgAQ&imagekey=!1e2!2sgkhj0iGMun0hkWJonxPS9A&hl=en&sa=X&ved=2ahUKEwitiffqquTyAhWmFFkFHfwGDZsQoiowCnoECEEQAw
Back then the diving was fantastic in a lot of places, but a lot has changed. Some of my favorite dive spots out of Fajardo (East Coast) are not that good anymore (boat diving access only).
As others have mentioned, the dive spots on the south west (Parguera) and west of the main island are some of the best. Culebra and Vieques are also good.
For such a big island most of the good diving require boat access.
Shore diving in Crash Boat Beach (Aguadilla) has always been good. And there are other spots just north of Crash Boat Beach... I can't remember the names right now.
El Escambron Beach is also good, but parking can be an issue. The last time I was there we actually paid a guide to drive us close to the put in (they have a special permit). When I was a kid we used to just park behind the Caribe Hilton, walk into the back of the property, and jump in with our scuba gear from their observation pier. It was a real "giant" stride.
I have been diving with Taino Divers from Rincon, boat ride to Desecheo. It was fantastic diving. That was recently... about 10 years ago.
It has been awhile since I have been back and I am glad to see this thread... We need to go back soon.
One thing to keep in mind, the island is big enough that it doesn't have the same feel as the smaller Caribbean islands (Bonaire, Cozumel, Roatan, etc.). I think that is part of the reason it is not always considered a dive destination.
I have never seen a true full service dive resort that will provide a full package including transportation, lodging, and diving. There are some high end resort that offer diving, but diving is secondary. You just have to be a bit adventurous and arrange it all yourself.
While I am talking about adventurous, driving in PR in the San Juan area may not for everyone, or at least that is how it used to be.