Poor little guy! Before you give him meds of any sort do consider that infants are especially sensitive to antihistamines like Benadryl. This drug also makes many people feel woozy and uncomfortable. Your son's ears might not itch after Benadryl, but he might not feel exactly better either. Here is some drug information for you to consider: http://www.drugs.com/benadryl.html
There are several possible causes for your son's itchy ears, but one simple thing that might help him is to cut sugar and processed foods (cereal, crackers, etc. made from white flour) out of his diet and/or out of your diet if you are breastfeeding. These things can promote yeast overgrowth, which is very, very itchy, and which can sometimes be a problem in the ear canals. Also avoid soap. Keep soap and shampoo out of his ears. These can be irritating and/or allergenic.
A helpful home remedy that often helps little ones with itchy ears of all varieties is white vinegar ear drops. Try this recipe from the Colorado Children's Hospital:
For itchy ear canal, use ½ strength white vinegar by diluting it with equal parts water. Place 2 drops in each ear canal daily for three days (Reason: restore the normal acid pH). (EXCEPTION: ear drainage, ear tubes or hole in eardrum.)
One other thing: you may already be doing this, but clipping your baby's fingernails very short should help keep him from drawing blood.
Finally, if this becomes a chronic problem related to allergies, homeopathic treatment is something to consider. It has helped other children (including mine) with allergies without using shots or prescription medicines.
Best of luck to you!