I assume you are talking about physical copies? Disclaimer that my answer is US-centric since that is my location and mostly focused on manga. Also, it is unlikely to be particularly helpful.

I almost exclusively consume things digitally these days, so my primary (legal, when available) source is the official publisher/streamer. That means places like amazon for kindle versions of things, bookwalker, etc. Also, I can’t remember ever buying physical copies of anime any time recently. If I can’t access it via legal streaming, I find other places to get it on the internet. In the before times (pre-streaming), conventions used to be the best place to find DVDs of anime, but I haven’t been to a convention in a long time, so I don’t know how true that still is.

For physical manga, my go-to back when I bought it was a local comic book shop. They had a decent selection of stuff, but they would also buy things on request. This was particularly helpful if they had most of the volumes of a series, but with a couple gaps. I used to walk by the shop on the way to the subway every day on my commute, and didn’t really think anything of it since I don’t really read Western comics. However, one day they had a bunch of Cardcaptor Sakura omnibus volumes on display in the window. That is what led me to find out they carried manga as well. However, two years ago I moved and am not nearby that store any more. The only physical things I have bought since, I got from amazon (TEIS LNs).

That being said, other than amazon (which will almost definitely have most of what you are looking for), there is gomanga which sells physical manga/LNs (they are the official store of Seven Seas). Barnes and Noble also has a pretty good manga selection. My last pick is pretty local, but if you are in the greater Boston area, Newbury Comics has a good selection as well with some convenient locations (even though their website is pretty bad).

…TIL that Anime Corner Store is still around. Haven’t bought from them in over 20 years. It’s been almost all Right Stuf since then. Which means I don’t really have any other leads that aren’t the obvious big corps (Crunchy, Amazon, etc.), sorry.

What are you looking for? Stuff directly from Japan? 25 years ago when I lived in the US, jlist.com was the place to go. Seems they’ve turned into https://jbox.com/ now, but otherwise seems the same as before … anyone know if they’re still legit? Used to be you could just message him what you were looking for and he’d quote you a price, but not sure if he’s still doing that though.