Give him a thorough wash in cool water, really scrub him. If it is something like grasses that is setting him off, washing him will relieve his discomfort for the short term. You can also fully rug him, and spray him in fly spray each day.
If the hives get really bad, you will need to get him injected with an anti-histamine. Hives can cause swelling of the airways if they get too bad, so you do need to keep an eye on it.
I had a gelding who was highly allergic to ant bites. He'd come out looking like the elephant man, all his nostrils swollen and his sheath would even swell up, the poor love! As a result, I always had a couple of anti-histamine injections ready in my fridge.