I am a military spouse living in Japan. We've been here less than 6 months and haven't personally made it to Tokyo yet. I have heard though, that the merchandise in the Japan parks is much, much different than you would find in the U.S. There are not lots of shirts, sweatshirts and ballcaps, and if they are there, they will run in sizes much smaller than your typical US sizes. A friend just went to Disney Sea and Tokyo Disneyland and said that there were lots of hand towels (the Japanese use these constantly) and stuffed animals as well as cell phone charms (another popular item in Japan).
Hope this helps some! We're planning to go next Christmas at the latest unless we get there sooner with a base sponsored trip, or if Spring Break happens to work out for all 4 of us to go.
My family took a trip to Tokyo at the end of December and I missed out <still kicking myself over it>. They took some pics of cool merchandise at Disney Sea. I was hoping to order it from Disney Sea since they didn't have enough room in their suitcases to bring back too many souvies. I'm not sure if they have a phone # to order merchandise like Disneyland Deliev-Ears.