Seems like there’s a new used bookshop in town, and it’s part of the Las Chicas complex. Antipixel’s Jeremy has this to say:
Across the courtyard from Las Chicas in Jingumae there is now a small but very interesting English-language bookstore called Intelligent Idiot (not a great web site, but what can you do?). It’s tiny really, but the woman who runs it has assembled a good and somewhat quirky selection of novels, photography & design books, and children’s books. The prices are surprisingly good (and I do mean surprisingly). It’s certainly worth a visit if you’re in the neighbourhood (just don’t buy that Helen Levitt book: I have my eye on that).
I’ll remind you that the nicest used English bookshop I’ve seen is Caravan Books in Ikebukuro.