I had the same problem as you....a low impact solution to your problem is to go to a pool and swim (freestyle or crawl, whatever you want to call it). Rotating your shoulder in 360 degrees with resistance is excellent, plus if you go slow, you can strengthen your shoulder withour doing harm. I did notice that if i swam for too long or tried too hard, i would be sore or my shoulder would pop out of socket briefly. I have recommended this exercise to others and it completely fixed their problem as well.
Also, to prevent injury to shoulders when boating, always stretch before getting in the water...just rotating your shoulder (like you are swimming) for a couple minutes will prevent early injuries when on the water. I noticed that i always hurt my shoulder within the first 1/2 hour on the water.
Side note....maybe your problem stems from a fundamental roll problem. Revisit your roll or your bracing technique. If you have really good form, your shoulder should never go over your head nor should it ever be more than 8-10 inches from your torso. If it does, you are putting yourself at risk to dislocate your shoulder. Everyone should practice good form and learn what a perfect roll should look like, no matter how long they have been paddling.....it helped me.