Is your son by any chance teething, or could he have an ear infection? Any "head" pain can get worse when you lay down.
If you think it's teething, try a dose of Tylenol before bed. My son also had great results with Hyland's Teething Tablets.
And Hyland's also makes Calmes Forte, which is a homeopathic remedy to help kids relax for bedtime. You can get it at Whole Foods, and most co-ops should carry it.
Consider running a fan in his room for white noise. (We run one in our son's room. It's just a little tabletop fan, and we have it turned so it's blowing against the wall).
Also, make sure the room isn't too hot, especially if your little guy is wearing "feetie pajamas".
Lastly, consider visiting a chiropractor. My babysitter's daughter was a restless sleeper until she had chiropractic care.
Good luck!