Hi Shan and thank you for coming to JustAnswer.com with your question.
There are a few things that could be other reasons for your son's itching.
One could be 'occult fecal leakage' which basically means that a tiny bit of stool (possibly less than you can see with the naked eye) leaks out. Also, passing gas can sometimes cause a similar problem.
Certain spicy foods can cause itching of the anus.
A yeast infection / rash can cause this - although that is something I'm sure you would be able to see clearly.
I know you've tested for pin worms already. You didn't write how extensively you checked. Studies have found that often infestations can be missed. Because the adult female dies after depositing her eggs, the false negative rate can be up to 95%.
Testing with scotch tape also has shown to have a lot of false negatives, with a sensitivity of only 50%, 3 examinations had a sensitivity of 95%, and 5 examinations had a sensitivity of 99%.
If the examination is repeated one to two days later there is a much higher chance of finding them.
Unfortunately there is the possibility of 'idiopathic' itching which basically means itching for no reason that we can find. It is possible that his doctor can try prescribing some creams to help relieve the itching if no source is found.
This website gives a whole list of possibilities, most of which are obviously not appropriate. http://www.wrongdiagnosis.com/symptoms/anal_itching/causes.htm
I wish you the best of luck and hope your son is feeling much better very soon.
If you have any follow-up questions feel free to ask them.
If you are satisfied with my answer please click 'accept' so that I can be paid. BONUSES and POSITIVE FEEDBACK are not necessary, but always appreciated.