So I followed the advice and took my son in to see an Orthopedic Surgeon in Tampa.
He took X-rays of both shoulders and deducted that the pain was due to "Little Leaguers Shoulder". My son has been asked to ice his arm at least 3 times a day and NOT do any throwing/pitching for at least 6 weeks, at which point we will see him again.
Thanks everyone for your comments and suggestions. It was what made me take him to the doctor in the first place :-)