uh, how far are you willing to drive?
Well, the one my friend always goes to in socal is the Book-Off here:
http://www.bookoff.co.jp/en/info/kaigai03.html
He's had some good finds at that store...like the Hamasaki Republic Mag for 3.00 in New Condition. But I think it was more luck because he goes all the time and checks to see what they have.
In SF...i think there's only the Kinokuniya...and that's not cheap/used...It's in Japantown...but I haven't gone there yet.
You're gonna be in both LA and SF? That's quite a trip!