If you're looking for a one-stop place for Funkey shopping, I recommend checking out FunkeyFever.com. And they have recently added the Funkey Plushies to their store!
If you prefer to shop in the brick and mortar stores, you might need to do some driving around to find the particular Funkeys you are looking for (the long-time Funkey players know this ALL too well after much wasted gas driving from store to store on our Funkey hunts!)
For the best prices on UB Funkeys, Walmart and Target are the places to go. Singles sell for $4.94 or so. The double packs of Chat Funkeys or Multiplayer packs are around $10.49. Kmart has a sale this upcoming week with the best prices yet!
I'll do my best to compile a list of which stores carry which series of Funkeys (and, please, everyone who has additional information or corrections, I'd love to hear from you through comments or email! Thanks!)
Dream State singles: Walmart, Toys R Us, KMart, Target, KB Toys, Limited Too
Speed Racer series: Target, Toys R Us
Series 1 & 2 Funkey singles: Everyplace Funkeys are sold including Walgreens
Chat Funkeys: Target, Walmart, Toys R Us
Multiplayer Packs: Walmart, Toys R Us, Limited Too
Funkeystown Adventure Pack (Mayor Sayso, Master Lox, Henchman, and Bones): KMart only!
Funkiki Island Adventure Pack (Pineapple King, Jerry, Native, and Sol): Target only!
But FunkeyFever.com has all of those, and when they get low on their stock, they work very hard to find what you are looking for!!