Aye, I buy mine in person from my local Kinokuniya. 
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In Japan, I go to Kinokuniya or Book Off.
There are some Kinokuniya stores in California, I believe, and probably in some other states, where thereās a significant Japanese population. Many used bookstores (if any still exist in the U.S.) likely have a foreign languages section. I did a search on Powellās Books and there are a lot of manga titles (havenāt explored further to find if they are translated or not): Search Results - Powell's Books
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Like @anon12500920 and @insu, I also usually buy in bulk from Mandarake. Shipping with DHL is amazing (they email and text updates automatically, and generally everything arrives ahead of schedule). Only issue Iāve had lately ordering from them is sometimes the payment method verification fails (I use a Visa card with a US address) and I have to call up my bank (the website gives you the number to call) and get them to whitelist the charge.
Still generally cheaper and better shipping experience than Amazon.co.jp.
If I ever want anything new instead of excellent quality used or Mandarake doesnāt have it, then I usually check Kinokuniya next.
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Iāve only used Amazon.co.jp for books. Costs for shipping seem to be minimalized on orders over about $100usd. Thereās usually an option for expedited shipping for an extra $5 USD. The difference in shipping speed for that $5 is nearly-life changing. I have had shipments arrive in less than 3 full business days, from Tokyo to Columbus doorstep delivered with the expedited shipping.
I imagine a Mitsubishi A5M heading down a runway outside of a warehouse when a warehouse clerk sees my order, rushes out with box in hand and chucks it up to the pilot right before they lift off, holding his hat to keep it from flying off Ghibli style. 
Changed plane type to one that actually appeared in Ghibli film
Whenever I go to Half Price Books, I check their foreign language section. There often isnāt much, if anything, that interests me, but I have found some stuff. I wouldnāt really know how to go about looking on their website for foreign-language books that arenāt for language-learning, though. And thereās also the Kinokuniya stores, but their selection of JP-language books is small compared to their ENG-language, and the prices are marked up enough that itās actually cheaper just getting them off Amazon or the Kinokuniya JP website with shipping, especially if youāre looking to get several.
Aside from that, I keep wish lists on Amazon JP, and Iāll usually buy from them since thatās easiest, but when they donāt have something available for international shipping, then Iāll start looking on CDJapan, Kinokuniya, Mandarake, Bookoff, YesAsia (which has free shipping on orders over $59). Mandarakeās best if they have everything youāre looking for in a single store, though, or else youāre paying for shipping multiple times since they donāt ship from a warehouse. If itās just one or two volumes, Iāll look on Manga Republic, but the prices there are pretty variable (though it is free shipping on everything).
If youāre fine with a ļæ„1500 proxy fee on top of shipping, you can check Yahoo Japan for cheap used copies and use CDJapanās proxy service. There are some other sites theyāll buy from as well, but thatās the only one I have saved (clicking on the proxy link for an item doesnāt always work, though you can still submit a request even if it doesnāt if you find the item on your own). Iāve used it a couple times and havenāt had any problems, plus you still get points on proxy orders and can use your points on them. (Update: Actually, now that Iām thinking more about it, Iām not sure if I did get points on the proxy items, but you can use your points on proxy orders.)
Bookoff has both a JP and US site, though I havenāt really used the JP site. The ENG site though sells sets, for $4-5 per book, and they have multiple options for shipping. The cheapest one at least depends on weight, but the once I used it, it was only $9, for 19 books.
You can also check eBay; Iāve gotten a couple sets pretty cheap off of there. Itās not that great for single volumes, though. And for manga thatāve been licensed in English, youāre much more likely to find those than JP copies. Some sellers will have cheap or even free shipping though, even international.
There wasnāt one at the one I went to in San Diego. Though there was a book-off in the same plaza.
Oh, book-off!
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Iāve never checked but Iād keep an eye on ebay. Surely such items must come up.
Also if you have a local Japanese community keep an eye on their buying/selling forums as well as community events such as flea markets. Example: ćć·ć¬ć³å£ć³ć
I also live in the US. Ebay is my go to because I can find low price stuff, free shipping. Many sets available. Book off is another option but they donāt have much stuff Iām interested in. And thereās kinokuniya, but I havenāt looked into them much at all. Lastly thereās manga republic which has the widest variety of manga but unfortunately what they charge costs as much as English translated manga, if not more.
So true! For whole sets, eBay can be great.
I second that for Europe! Pretty good prices and not a bad variety either. They came to me (Greece) in about 7 to 10 days, I think?
Also, I wishlisted some yotsubato volumes and sure enough they got back in stock after 2 weeks or so. 
I use both Kinokuniya and CD Japan in getting physical manga in Japanese.
I get digital from bookwalker, but hate that the furigana is kind of blurry/not high quality.
Iāve used Mandarake a few times, and they were good, yeah, but beware that theyāre pretty strict with order cancellations. I once tried to buy manga marked as 18+, marked so purely for the fact that it had āvirginā in the title, despite there not being any sex or violence in the manga itself. They canāt take PayPal for 18+ products because they require proof of age, so I tried to pay by credit card. Because it was a foreign credit card, they rejected it. Because a week went by while I was trying to pay without anything going through, they cancelled my order and terminated my account. Am now mildly terrified of trying to make another and them, idk, IP banning me or something. 
I now order everything from Suruga-ya (second-hand) or Toranoana (new) via Zenmarket. I donāt tend to buy full sets myself, but I think Zenmarket have some in their affiliate store.
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book-off still doesnt ship internationally?
I wish it did, when I was in japan it was crazy seeing lots of fullsets for 500yen in almost every store. The problem there was having space in case I wanted to buy them 
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Oh geez, I canāt imagine what they would do with xxxHolic 
(which is a shonen manga with no sex, just a slightly unfourtunate title)
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I suppose itās my own fault for trying to buy a manga titled Cherry Magic! Thirty Years of Virginity Can Make You a Wizard?!. I can excuse the stupid title in my head because itās actually a really sweet story about self acceptance and how everyone moves at their own pace, but I wonder if publishers and such consider even talking about the concept of sex to be mature content, now. 
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I recommend CD Japan. Here in Australia manga are $25 - $30 each. CD Japan had the same stuff for $5 each. The only expensive part is the shipping (about $32 delivery). Still waaaaaaay cheaper than if i bought them here (and they only sell in English anyway).
Yeh thatās what I found with Bookwalker too. Pretty poor imo. Even when you zoom in the picture is blurry. Not worth it.
I use CDJapan a lot for bulk buying. Pretty good prices and shipping is always really fast and not terrible. For smaller batch buys like just a book or two I usually go with Manga Republic. Both sites I have nothing but good things to say about them. Everything arrives within a week usually and in great condition. If you are trying to find something older that isnāt in print anymore you can use CDJapan and theyāll go out to book stores and try to find a copy for you too.
That does sound sweet, and I like that itās about a 30 year old rather than a teenager. Darnit now I want to read itā¦this is gonna be embarrassing trying to get a copy. 
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Ohoho? I converted you? All according to keikaku 
There is a very good drama adaptation of it, if you feel like getting in some listening practice instead!
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