depends on your interests...
Oedo Onsen Monogatari (try Google to find info in English)
Sony Explora Science http://www.sonyexplorascience.jp/english/index.html
Ghibli Museum (if you can get tickets)
explore the basement food halls of large department stores like Isetan, Takashimaya, Daimaru, etc to see all the pretty food & sweets (especially the beautiful wagashi) & super expensive bento
cat cafe ;)
huge malls like the underground ones (including Tokyo Character Street) linked to Tokyo station, or Tokyo Skytree
Namja Town at Ikebukuro - Gyoza Stadium & Ice Cream City
& you could always hop on a fast train for a daytrip to somewhere that isn't raining?
I must admit some of the best things to do on a rainy day might just be a number of the museums... the Tokyo Metropolitan Museum of Photography is a personal favourite, as is the Museum of Contemporary Art (MOT) although that one depends more on what they're showing. Other than that, I agree with wanderingcat - depachikas (the underground food courts) are fantastic!
You might be able to arrange a short trip to a sumo stable through your accommodation as well, they're definitely worth the trip.
and of course... karaoke! (if it's still raining at night)
#3kitebo has been a member since 30/12/2010. Location: Netherlands. Posts: 10