I visited the Tokyo branch of Kinokuniya several times on my last visit to Tokyo because there are only so many bags of books you can carry on the train back to your hotel. They have the best collection of Japanese craft books in the city. Take the elevator to 2F for craft books and walk to the back wall. Be prepared to pull out all the books since the titles are almost always in Japanese and I have a trick of half pulling out several books at a time to check covers then push them back and move along the shelf....this is why you need time here. When you're done take the elevator to 3F for magazines like Cotton Time and Cotton Friend which are located in the back right corner of the store!
You'll find Kinokuniya in Shinjuku and its open everyday 10am-8pm....perfect for some after dinner shopping. Take the South exit and walk towards Takashiyama, walk behind Tokyu Hands and its there straight ahead of you via the walkway.....and this is how they wrap your bags in the rain...practical and cute.