Have you changed his pillow? I have to change my pillow every 4-6 months, or the dust that builds up gives me bad headaches, watery eyes and congestion. I buy hypo-allergenic pillows (which are just a few dollars more than the regular ones), and allergy covers for them (which can be washed).
Don't forget to wash any stuffed animals regularly, too, as well as change the filters in the air conditioner and dust his room.
Allergy testing is a good idea, too.
I hope he feels better!