D.,
Not all allergies are created equally. Food allergies can be tricky and have several degrees of intolerance. I have a friend who took her daughter in to be tested for allegies because she broke out in hives every time she drank milk. The blood test showed no allergy. It didn't make sense.
I would recommend a food elimination diet. There is a great book called "Is this your child?" by Dr. Doris Rapp and it explains exactly how to do it, step by step. It is not invasive at all - which is NOT what I can say for a blood test or scratch test that aren't always accurate.
Basically, you take out possible allergens in your son's diet and then slowly one by one add things and see what the reaction is, if any.
Please let me know if you have any questions, I have been there done that with allergies and feel like we've got a pretty good handle on the situation in our house.
Best of Luck,
B.