If you love shopping and dont mind walking around and taking the train a lot, I'd recommend going to Harajuku and Ginza.
For sightseeing, its okay to go to Mt. Fuji but with the cold and unpredictable weather, you might be able to go up to the first station only(like us!) Also it's better to get a package tour for sightseeing as having an English speaking guide is essential for you to know the history of the places you see as well. We've also been to Kyoto and I can say that its one of the best places to go sightseeing in Japan because its the cultural center.