I studied martial arts for 10yrs. I also taught it for 6. I would have to say that the most meaningful gifts were from the children.
Here is my suggestion. You son is old enough to write. So, why not have him write a thank you letter to his Sensei telling him how Karate and his Sensei in particular has helped him or changed him for the better. You could scan it or even take it to Fedex (or go to snapfish or kodak) and have them do a layout with your son's picture (or picture of Sensei and your son) and his hanwritten thank you! If you feel you want to include a gift card that would be nice too (I personally like Starbucks). But, speaking from experience, that personal thank you would be more than enough.