Let me start with this link to all the Donguri official shops in Japan and then move on to my personal experiences and other shops
Tokyo Station’s Character Street, two minutes away from Tokyo Station’s Yaesu exit, inside First Avenue Tokyo Station, you can find the shop named Donguri Kyōwakoku.
Find more info at the link, including detailed instructions on finding the shop:
In the Akihabara shopping hub of Tokyo there is a shop called Kotobukiya that has many of the same items that you would find in the other Ghibli stores listed here, you can find them on the first floor in the back corner
In Tokyo Shibuya area the Mega Don Quijote has a decent selection of stuff on the second floor toy area.
28-6 Udagawacho, Shibuya City, Tokyo 154-0042
In Kamakura Komachi Dori Shopping Area, the Ghibli shop technically has two floors but they are two side-by-side boutiques. Here there are a few items that I didn’t see elsewhere
〒248-0006 Kanagawa, Kamakura, Komachi, 1 Chome−5−6 松秀ビル
In Nakano Broadway
And of course if you are at Nakano Broadway you wont need to go far to find some truly outstanding stuff both new and vintage. Start on the second and third floor. I saw a large, extremely rare hebikera (flying centipede) toy/model from Nausicaa and Laputa: Castle in the Sky robot stackable game
Google “Ghibli shop Kyoto.” Two locations will pop up in Gion neighborhood. They both have unassuming store fronts but are surprisingly large on the inside, especially the one with the cafe (the Northernmost of the two). They have many wonderful items at various price points that puts the Tokyo Ghibli Museum gift shop to shame. It is a short walk between the two shops and I found unique items in each so visit both if you can! And if you’re not interested in Ghibli then disregard. Happy to answer any questions
Donguri Address: 363-22-2 Masuyacho, Higashiyama Ward, Kyoto, 605-0826, Japan
Ghibli Studios Shop Kyoto Address: 〒605-0862 Kyoto, Higashiyama Ward, 清水2ｰ224