I've seen quite a few threads looking for Japanese MLP plushies. I read Japanese fairly well (though I'm not a native speaker!) and I have experience buying goods on Japanese sites, so I made this quick guide.
Japanese Auction Sites*
Mbok - Mbok is a popular auction site. It's mostly for things like clothes and electronics, but you do see toys there sometimes. You need a deputy (see below) to buy from there.
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Y!J Auctions[/url] - Yahoo! Japan Auctions is a Japanese auctions site much like eBay and great for buying anything you could want, pretty much! Even G1 Japan exclusive items pop up here sometimes. You can search on Y!J from the main bar, or go to the specific sections to narrow it down. The sections are on the left sidebar.
おもちゃ = Toys (sixth down)
ホビー、カルチャー = Hobby items (seventh down) (this section is mostly for garage kits and crafts, so finding them here is unlikely)
漫画 = Comic books (third down, second option) (Japanese language comics)
From within comic books, 同人誌 (Doujinshi, aka self-published\fan goods) (You can find non-official artist items here)
Here is a list of search terms you can C&P into the auction sites. Trying the English terms works too sometimes.
マイリトルポニー = My Little Pony (Also try "MLP")
フラタシャイ = Fluttershy
ラリティ = Rarity
トワイライト = Twilight Sparkle
ピンキーパイ = Pinkie Pie
アップルジャック = Applejack
レインボーダッシュ = Rainbow Dash
のルナ = Luna
トリクシー = Trixie
If you want any other character names added, ask me and I'll get them up here!
Other stores*
Mandarake - I highly recommend Mandarake. It is a great shop for purchasing animation production goods (like cels; I've actually bought MLP cels here before), character goods, doujinshi (self published comics, often fanworks), toys (like Blythe, Sylvanian Families, and Kaiju toys), figures (like Figma, Super Action Statue, Real Action Heroes), and other animation and pop-culture related goods. The chance of finding MLP stuff here is very low but I include it anyway. Do note two important things: 1) they DO ship directly outside of Japan to most countries, so no deputy is needed, and 2) though this is true, searching with non-Japanese search terms yields very little results. Just try searching for "JoJo" vs "ジョジョ" for an example. Toys are often cheaper here in very lightly used condition than at Western stores or other Japanese toy shops like HLJ.
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Mlp Official EC Shop[/url] - Official Japanaese MLP shop. Does not ship to the USA. You'll need a deputy.
Currently they have all the larger Japanese plushies, at 2,625円, or about $26USD.
* Alice-Books is a doujinshi market that sells mostly furry and teratophilia (monster) books and goods, and you can find MLP stuff there, all fan goods, like keychains and artbooks. HOWEVER, I'm not linking there as a lot of the fanbooks are adult (as in 18+) in nature. You do not need a deputy to buy from Alice-Books.
DEPUTY SERVICESJaponica - My personal fave. Highly recommended.
Celga - I've had a few issues with Celga in the past but generally pretty good service.
I personally do not recommend Rinkya or Shopping Mall Japan due to poor service.
If you have any questions or want me to add any more information or search terms, please do ask.