Vintage QOO, Shibuya
QOO is super well-curated, so you can either go in to browse or go in with a mission. There's a small chance there will be a line outside, but it goes quickly, and it's worth the wait.
Komehyo, Shinjuku
With several locations in Tokyo (I checked out many of them), there are so many opportunities to strike gold.
Kindal, Ginza
There are several Kindal locations, but the Ginza one was particularly impressive, especially if you're looking for handbags.
Ragtag, Harajuku
Amazing vintage spot in Harajuku with a great men's selection, too.