Most of the big Ginza department stores carry limited stocks of Japanese single malt. Overall, I was quite disappointed by their selections when I visited. They are really not much better than two of the better local supermarkets round where I live. Although it is a fairly reliable source if you are on a flying visit, I wouldn't advise a massive detour to visit the Ginza. The selection is pretty much limited to Yoichi, Miyagikyou, Yamazaki and Hakushu, with some Karuizawa and Fuji Gotenba occasionally thrown into the mix. Some of the stores carry miniatures, which might be a good way to sample some of this stuff without spending a fortune.
Usually, the liquor sections are in the department stores' basements. If you go to the Ginza on a weekend you will have a more restful shopping experience because they have taken the very civilised decision to shut it off to traffic.
There is no clear winner among these shops, so I will let some photos say several thousand words. Click on the photos for bigger images:
Various ages of Yamazaki, various ages of Yoichi, some Karuizawa. (Oh, and by the way, some of that highly sought after Old Parr's Superior up at the top there, methinks.)
They had these miniatures (only Yamazaki is a single malt) and a small cabinet with a very limited range of proper bottles. I have not checked out their main store further north in Nihonbashi yet.
A fairly reasonable, if standard, selection, plus a couple of miniatures.
Yoichi, Miyagikyou, Hakushu, plus various ages of Yamazaki.
Yamazaki and Hakushu miniatures.
MeidiyaI have included Meidiya, which is not a department store but a foreign luxuries shop, in this Ginza section. It is further up Chuo-dori on your left, if you are walking north, near the junction with the Tokyo station street. It has a big "My" on its blue shopfront. Meidiya carries a fairly good selection of Japanese single malts, as well as a lot of foreign wines and spirits, but it is not startlingly better than the department stores to the South.
Couple of different types of Karuizawa, as well as Yamazaki, Fuji-Gotenba (?) and Yoichi.
Location: Chuo-dori, Chuo-ku, central Tokyo.
View location on map of single malt stores.