Have you checked to see how he sleeps at night? Massage can also help the muscle tension that is making him prefer that side, or you could also take him to a chiropractor for a gentle adjustment (yes, they even do newborns!)They also might have a few recommendations for you.

my child had torticollis, a tightening of the muscles on one side of his neck. he was born with it. he went through a few months of physical therapy to strengthen his neck and was just fine. it is fairly common, my son got it from low amniotic fluid and having his head stuck in an akward position inutero. we noticed it when i went to a breastfeeding expert who told us the reason he wasn't eating was because turning his neck was hurting him. He has had no problems since his therapy around 3 months old.