Thanks for the advice. I've started scoping out shots in preparation for the trip!
You've got to go up Mori Tower in Tokyo at night. Daytime, of course, is good too, but nighttime views are spectacular and you can take endless shots of Tokyo from above - from 180 degree angles. In Yokohama go to the Landmark Tower in Minatomirai. Same amount of awesomeness.
The rest depends on how long you are planning to be there and how you are planning to spend your time. But the two locations above are an absolute must.