I had this problem too. Do you throw your yarn with your right hand or do you hold your working yarn in the left?
I used to knit english style and my shoulders would hurt quite a bit, to where I didn't want to knit anymore. My dad suggested I learn continental (which isn't too hard to pick up). There is less movement involved in the shoulders, and it works so much better for me.
If you don't know how to knit continental and would like some help learning how, Amy has wonderful video's on just about anything you might come across in your knitting here.
One thing I also did was to change the chair I sat in. I find if I am slouchy in my comfy couch I end up paying for it when I knit like that. :shrug:
Hope this helps and your shoulder is feeling better soon!