If you're looking for Pokémon plushes, Toys R Us always has a bin with whatever is the latest few American releases. Some Targets and Wal•Marts do too.
Locally run toy shops or smaller chains (such as Puzzle Zoo, though I don't know if they're around where you're at) have a wider selection, though the stores themselves are harder to find because the recession has almost destroyed the brick-and-mortar toy store.
For Japanese-only ones, like that Reuniclus or Klinklang, your best bet, during normal times of the year, is a store dedicated to Japanese stuff, such as Tokyo Lifestyle. If there is an anime convention near you, and you feel it's worth visiting, there will be almost every Pokémon plush ever manufactured for sale there.