Unfortunately there isn't an easy answer to this. The best place to buy almost any Japanese collectible, including Nyan Nyan Nyanko plushes, is Yahoo! Japan auctions. They have a reasonably good selection of plushes and much lower prices than Western sites. There is also M-bok, another auction site, also with good prices but their selection isn't as good.
To purchase items from Yahoo! Japan auctions requires a shopping service (I like Noppin) which is a business that for a small fee will act as a middleman and help you purchase goods that are only available in Japan. All the steps required can be a little intimidating at first but it really isn't much more difficult than shopping on e-bay.
Speaking of e-bay...they're also a good place to find Nyanko plushes. There are usually only a few Nyan Nyan Nyanko plushes for sale at any given time but if you have patience and check daily you can find some great things. I would put eCrater in the same category as e-bay.
Then there's My Nyanko World. I haven't ordered from them so I can't give any sort of feedback as to what sort of business they are. The prices are high, for sure, but they look like they have a good selection. Anyone bought from them?
As a side note: When looking on Japanese sites for Nyan Nyan Nyanko plushes the search terms you want to use are "にゃんにゃんにゃんこ" (Nyan Nyan Nyanko) and " ぬいぐるみ" (plush).
Hope this helps! Good luck on your hunt for cute kitty plushes!
