Ghibli Museum, Tokyo DisneySea, Universal Studios Japan, Tsukiji Fish Market, and Tokyo Skytree as well as a hot springs are hopefully high on your list.
My one piece of advice would be if you are visiting Japan, try to go somewhere besides Tokyo. Anyway is fine, really. Otherwise, you run the risk of basing all your impressions of the country on a single city, which is like judging the United States on, say, New York City. Try to travel around if possible and visit other cities, towns, and the rural countryside.