Getting Around Tokyo & Kyoto?

I will mostly be part of a tour but we have about 1 1/2 days in Tokyo and 1 1/2 days in Kyoto.

In Tokyo, what is the best way to get around to all the major sights. We are staying in a fairly central place. Is Tokyo walkable or do you suggest we take a subway or train (is there a difference)

In Kyoto, we are staying directly across the street from the big train station. What are fun places to see that are walking distance from there. Also is the Gion district walkable from where we are staying?

What to see in Tokyo and how to get there:
http://www.japan-guide.com/e/e2164.html

Tokyo sights are best accessed by train or subway, although it is possible to walk between some of them on foot.

What to see in Kyoto and how to get there:
http://www.japan-guide.com/e/e2158.html

Kyoto sights are best accessed by subway, bus and taxi, although there are some nice walks that let you combine several spots.