When in Tokyo, we tend to do the usual tourist stuff: Disneyland, Shinjuku, Shibuya ... temples, etc...
Here are a few of my favourite things to do whenever in Tokyo:
1) Sumo Tour: Tokyo Tournament & Chanko Dinner Plan (12,700 yen)
Its an amazing, short, 4 hour tour by JapaniCan. If you love Sumo you would be extra happy, even if you do not, its an amazing way to get in touch and experience it firsthand.
Sumo tournaments go around the major cities, they rotate and I think there are 6 tournaments, with Tokyo hosting it twice a year. Each time, its about two weeks long, and you just pick a day, hopefully it coincides with your trip.