Steph:
Welcome to mamapedia!!!
Are his eyes bloodshot as well? Do they itch during the day? Is it possible he has pink eye/conjunctivitis?
You can have his blood drawn and have them test him for allergies. However, he has to be anti-histamine free for 72 hours or more so the tests are accurate.
You can make his bedroom as allergy free as possible. Go to Target and purchase items like these...
http://www.allergyguarddirect.com/?gclid=CJjvp4KtqLYCFYbc...
Make sure there is an air purifier in his room. Then keep whatever allergens - dust, dust mites, etc. down by vacuuming his room daily. If there is carpet in his room - sorry - if he has allergies like that - it has to go. Get hardwood floors put in - they are easier to clean and don't hold allergens like carpeting.
If he has drapes - take them down and clean them. Replace them with blinds instead of fabric - again - won't hold the allergens like fabric....
Before he goes to bed - you can give him children's liquid Claritin or Zrytec. Check with your pharmacist to ensure that he is old enough and the right dosage. You can also check with your pediatrician.
good luck!