The Jinbocho district in central Tokyo is a second-hand book and vintage manga paradise and of course it's featured in my Tokyo Geek's Guide (see p. 46-47).
The very first spot in my otaku walk was Shosen Bookmart, one of the best shops in the area for comics and light novels for girls, with lots of shojo and BL manga.
Alas the bookstore has closed even though the giant billboard on the roof is still there.
There is actually another Shosen store in Jinbocho: Shosen Grande 書泉グランデ. It's on the second block from the defunct Bookmart, past Warhammer (also featured in my walk).
Unfortunately the focus of this store are hobby-related publications (that's why I left it out of my book) but if you are into pro wrestling, military, the outdoors and especially trains and railways it's well worth a visit.
Shosen Grande, 1-3-2 Jinbocho
Open 10:00-21:00 (weekdays), 10:00-20:00 (weekends and holidays)