The travelsafe.pr.gov is the official site. I found the requirements a little confusing since one paragraph mentions PCR test or Antigen but then the statement at the bottom only states PCR and filling out the form seems to indicate only PCR is accepted. We had a 12 hour layover so we left the airport and our son (6) is the only one not vaccinated. We did an at home allume test on the boat in St. Thomas (we were flying back through SJU after our charter) and they seemed to accept it. It at least worked for us getting out of the airport and we're now back home. I can confirm though that for my wife, just filling in the info with the vaccination card was all that was needed.

I think if you aren't leaving the secured area then you do not need to upload anything, but am not 100%. I just know we didn't have to show the QR code we got from the site until we left the secure area after getting our bags. Easy enough to fill out the site though so might as well to avoid any issues if you can't get a confirmed answer.

We just got back early this morning, so this info is current based on our experience just yesterday 7/31/2021.