Hondarake is a second-hand Japanese book store in the city that I like to visit before I head to Kinokuniya.
I won't go so far as to say they're cheap, but prices are reasonable. One thing though, if you plan on coming back another day hoping to find it cheaper, bad luck. Prices there are as is and it'll probably be gone by the time you come back.
That said, the stuff there isn't amazing. You'll have to search long and hard before finding something that is interesting to someone who's only interested in the Japanese pop culture. The things that are good won't be there more than a week, but most other things will be there for a while, so don't expect too many new things every time you visit.
Shop owners are friendly, and they do have sales from time to time. Give it a go if you haven't already, you might be able to pick up some bargains.
TL;DR prices are ok, goods are ok, more for natives, but give it a go.
Japanese Book shop. They are so hard to find. Managed to find this shop by word of mouth. Excellent selection of books and my favourite Comics. They even have a reading section where you pay a small amount of money and read all the comics you want. also they have all interent access. One stop Jap shop for books. Owners are always there they are the most friendliest people, Aragato. :)
The pricing is really reasonable for the items for sale along with being in almost mint condition. The customer service is friendly and polite giving a calm and friendly environment for book reading.
Approximate cost: $10
furuhonyas can be fun if you're into the Japanese stuff. I love picking up couple of dozen volumes of mangas and getting a fat discount ! I'll also check this place out thx !