You could definitely spend a week in Tokyo and only scratch the surface. I stayed at the New Otani hotel which was Blofeld's HQ in "You Only Live Twice"

A trip to Kyoto is also definitely worth it - if you do that, I'd think about staying at least one night in a Ryokan (traditional Japanese Guest House) -
see for instance http://www.kyotoguesthouses.com/. I stayed in one called Tamahan which has the advantage that you get your own traditional Japanese bath and don't have to share with the rest of the guests.