I am going to share my favorite place to shop in Tokyo with you: Hanjiro in Harajuku.
Hanjiro isn't your regular vintage store it is a mix of recycled, reconstructed and new clothing. They also have wonderful accessories and footwear and in addition to that you get endless fashion inspiration by looking at the incredibly stylish customers shopping there. Hanjiro has stores in all major cities in Japan - each featuring unique interior design. In the two floor Harajuku store the ceiling is lined with white chandeliers and on the walls you find framed pictures of jesus and mary.
On the website you can view all the different Hanjiro stores in the 'SHOP' section. They also have a webshop where you can have a look at some of the pieces they have in store - if you manage to navigate through the Japanese only menu^o^.
Here's what I bought there: