My three-year old and her daddy are both allergic to cedar, grass, and dust mites. Here's what we've found to be helpful:
Change your HVAC filters frequently. (You can buy special three-month filters, otherwise, change monthly.)
Wash his hair every night before bed. (The dust or pollen or dander or whatever he's allergic to gets in the hair, and is then next to his face all night. This was the last step a good friend of ours needed to get their son off of allergy meds altogether. We wash our daughter's after school days, days when her allergies have been especially bad, and days when she's spent a significant amount of time outside. Every other day, at the LEAST, often every day.)
Dust-mite covers for the pillows and mattresses. National Allergy Supply, at the recommendation of DH's allergist. (www.natlallergy.com)
And you might want to check out the website for the American Academy of Allergies, Asthma and Immunology. They have a counter for the previous day's ACTUAL pollen levels. Keep an eye out for days when your son is especially bad, and then check out the levels for that day. It's not for a diagnosis, of course, but it might help you find a correlation. (http://www.aaaai.org/nab/index.cfm?p=pollen)
Hope this helps, and your little one is feeling better soon!