First of all, we need to address whether this nipping is just a behavioral issue or whether it occurs from pain.
Does he only nip when you brush a certain area? Try running just your bare hands over it. Does he still nip? Now gently and I mean very gently press. He may just not like being touched there and you'll have to discourage the nipping. But if he only nips when pressure is applied, he may have hurt himself. Its hard to say over the internet, but I'd recommend maybe getting an equine chiropractor out to have a look at him.