http://www.bwy.jp/2007/07/jack_road_is_one_of_the_bigges.html
If you could only go to one place go here. It is by far the biggest place I have found over the last couple of years going to Tokyo once a month. It is nestled in the midst of a mall that sells Anime stuff, so that by itself is interesting. Everything you could think of you could probably find here from Vintage Omegas to current Pateks.
There are small shops here and there in Shinjuku, on the Kabuki-cho side and the Ameyoko Arcade. I am not a Ginza sort of guy so have not really visited any ADs there.