When does he do it? Look and watch and see if you can find a 'trigger'. For example, if it was a bit issue, when you pull on the bit, he will do it. If it is a teeth issue, when he tries to eat, he will do it then. Find the pattern. If you find the pattern, then you might be able to find the problem, and thus, a solution. I don't mean just watch where he does it, such as 'in a pasture' or 'in his stall'. I mean what is he DOING when he tosses his head? Eating? Drinking? Walking? Something along those lines. It may take some time, but there is always a reason. Spend some time with him doing nothing but watching him. If no luck, try working with him and seeing what happens then.
~He knows when you're happy
~He knows when you're comfortable
~And he always knows when you have carrots.