My very favorites are Otaku Republic and their sister site Manga Republic. Everything is in Japanese.
For English translated manga and novels, I have purchased on EBay from other collectors, Amazon, and RightStufAnime. 1 reply
Amazon, Barnes and nobles (idk if I spelled that right), and bookwalker. You can also try Ebay but I kinda have trust issues with it since it's not always 100% reliable reply