Well, otokichi.com (they have an english-language section) only sells CDs and games, but I've ordered from them and they're great. They also have a middle-man service, where you can order stuff on amazon.co.jp or wherever through them. sasugabooks.com has some stuff too. I believe I ordered from them once years ago. They go to cons a lot. Apparently you can buy things on en.rakuten.co.jp now, too, but they're hard to search through in English. If you can visit nyc, you can go to book-off and find stuff for a couple of bucks. HIGHLY recommended, I find stuff there all the time and it's usually in great condition. Maybe you could ask someone if you can give them a laundry list of manga to search for. I'd offer to do it but I won't be here for a couple of months... Oh, kinokuniya has stores that sell new stuff, too.
Just out of curiosity, what manga are you looking for?