It's hard to answer the question without knowing what your interests are.
Some people might want CDs or magazines or manga that you can only get in Japan. Some might want some fashion items (Japanese streetwear, Porter bags, sneakers). Some people might want food or anime action figures or electronic gadgets from the Akihabara area of Tokyo. Then there are those who prefer traditional Japanese souvenirs like a yukata or chopsticks or calligraphy scrolls.
Tokyo has so many unique things, it's hard to say what souvenirs would be interesting to someone without knowing their interests.
Maybe you can just ask him to take you with him to Tokyo so you can pick your own souvenirs.
