When checking out of Port Orleans Riverside, you can absolutely use
Resort Airline Check-In. This service is offered to WDW resort guests when flying to a domestic location, including Puerto Rico.
American Airlines does offer this service. You'll be able to check your luggage at Port Orleans Riverside as well as get your boarding passes printed.
The Resort Airline Check-In desk is open from 5:00 am to 1:00 pm daily.
Please check in at least 3 hours prior to your flight.
This service is operated by a third party, not Disney. Thus, it does not matter where you actually purchased your airline tickets. I have used this service many times, even when my tickets were purchased directly with the airline instead of via a Disney vacation package.
I hope this information is helpful!