>>29356380EBay. There's one particular seller on eBay I adore, been ordering from them for years.
Official Pokemon Center store now that it's back in the US. You can sometimes find official stuff on Amazon from Japanese sellers, just have to check the seller reviews.
For plushies in general, OtakuMode, Build a Bear,Amazon.
Most "valuable" Pokemon merch is probably the huge Lugia with Pikachu on his back from the Pokemon Center back in 2001, the huge Pokemon Time Wailord and Gulpin, and the shiny Gyarados. But I hear the large Suicune and Raikou go for a lot now (these are just large not the life size beasts.) Original Rotoms, too, but those should go down with the surge of rotom merch on the horizon.
I check Pokeshopper almost daily.