I’ve only ever once bought them online because it was an edition that was exclusive to this retailer.
Apart from that, I’m always buying locally from the same store, from the nicest Manga selling lady in the world. She’s been running her section in that very store for as long as I can remember, and we get carried away talking about all kinds of things more often than I’d like to admit. That’s why my 5 minutes of “I’m just gonna pick up [whatever] real quick” and generally last about 30 - 45 minutes.
Many years ago I bought my (sometimes used) manga books from my local (really small and absolutely cool) science-fiction and comic-book store in Würzburg (Germany). The comic-experts in this store could always give me ideas what to read next :).
Later my main source for manga books were Thalia stores, Online comic-book stores and sometimes Ebay.