Hi Jake
Two that I can recommend in Fajardo are Casa del Mar and Aqua Adventrues. Both have multiple trips/day and I've had good experiences with both. They do trips to both Culebra and Vieques as well as other areas east of Puerto Rico.
The dive shops in San Juan also regularly arrange boat dive trips to Culebra and these leave out of either Fajardo or Ceiba. Shops that I would specifically recommend are Casa del Buzo, PRDive.net, and Scuba Dogs (only in Guyanabo, not the one in Escambron which is a training facility).
Don't let me dissuade you from going to Culebra -- it's a great place. If you do, I highly recommend Culebra Divers as they will have many trips not available from the PR-based places -- particularly on the eastern side of the island where the reefs are pristine. If you contact them, ask about their fluoro diving trips -- if you haven't done it before, it's really outstanding.
Tourism is still depressed here so you might be able to get one of these shops to set up a dive to a specific location. Culebra has too many great dive sites to mention but you can see a map of some of them here:
https://www.google.com/maps/d/u/0/viewer?msa=0&mid=1gWoryRmbWhMR9hcm3AzROXU4NLc&ll=18.312016650784287,-65.30927249999999&z=12
The sites west of Culebra, besides being closest to PR, are also in a marine preserve but the eastern sites are at least as nice and with far fewer divers. This is particularly true of the ones north of Culebrita (little Culebra).
You can get to Culebra using the ferry out of Ceiba for less than $5 but check on the COVID requirements first. There have been several big changes to COVID regulations the past couple of days (and the web site might not reflect those changes yet). If you have a vaccination card, you might not need anything. I suggest calling the ferry terminal directly when you're close to going so that you can have the latest info.
Anyway, the first ferry leaves Ceiba around 6:30 AM and the last one leaves Culebra around 4:45 PM -- plenty of time for a 2-tank dive and, of course, without a post-dive wait before flying.
I hope this is helpful but let me know if you would like any more info.