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The best Japanese stores to buy imported goods are usually Kaldi, Seijo Ishii, and Gyomu Super. Local Cuisine ingredients are usually available in the region-specific neighborhoods. Korean: Shin-Okubo / Chinese: Yokohama, Ueno, Ikebukuro / Indian: Nishi-Kasai.
In expat areas like Hiroo, you can find a shop called National Azabu. Costco is great for American goods.