Liquor Mountain (chain), Yamaya (chain), Shinanoya (chain), Hasegawa, Mejiro Tanakaya, Yobobashi Camera (Department Store), Bic Camera (Department Store) are all places to check out. Expect to find WT12 and EW12 all over. Blantons Red, Black, and Regular Gold are harder to find but you won't not find one on your trip. Takara Golds are super hard to find these days. WTMKs used to be everywhere but now they are harder to come by. If you want Japanese stuff, go to Life Vacation Ginza and bring your passport. It's not retail but it's the best prices I've found.
Bar wise, you have to go to Bar Benfiddich for cocktails. Also the SG club. Whiskey wise, go to Ken's Bar. If you're up for a trip to the middle of nowhere for maybe the best bourbon selection on the planet, go to GEMOR. If you can, I HIGHLY suggest going Yamazaki. They do a lottery system for tours now but even if you go to the tasting bar, it's worth it. You can try unreal pours like Hibiki 30 and Yama 25 for like 25 bucks each.