I was in San Juan when a student flew me down to do his OW checkouts. There are a couple shops in San Juan that dive off of the city but it's a real crap shoot due to the weather. That's also hurricane season and being on the north coast, things can go from to good to bad with heavy surge and surf quickly. When I arrived there were 6 ft waves breaking off the beach and due to that and that a storm had come through the day before, we went to Fajardo for the 1st 2 dives and Palmas for the next 2 the day after.
Nice sites and once the DM saw we knew what we were doing he indicated he was taking the group this way but if we wanted better stuff to "go the other way and waved bye bye to us. See you in an hour and swam away with the group."
The other shops go to or are in Fajardo or Palmas and if you do that you can forget about doing anything else that day. The east coast and south are better and the most popular.
As for exposure protection, I would never go in the ocean without full body coverage. Especially where there is a chance of surge kicking you into the coral or reef. You also have jellies to worry about. A full body rash guard (skin) would be ok but the water temps, even being in the 80s would see me bringing my 3 mil.
How old are your sons and how cold do they get? It's not just the water temps. The ride out can be very windy and chill someone quickly between dives.
Scuba Dogs and Aqua Adventures look like they offer guided dives off of San Juan but based on the website the guides are guides and not your own private DM. You should not expect anything from them other than to point things out and you are responsible for your own safety.
If you want more than someone to follow around, you need to call the shops and make separate arrangements for yourselves.
I would love to to go back to PR someday and dive the south and west coasts.