If you don't want to pay eBay prices, your best bets are:
1) GameStop. Here is the page for their used GameCube wireless controllers:
http://www.gamestop.com/product.asp?product%5Fid=900532
Out of stock online, but you could try your local stores. Now, like the page says, this is for ANY wireless GameCube controller, so you'd have to call ahead to make sure they actually have WaveBirds and not 3rd party controllers.
2) Large discount department stores, like Walmart and Target, that sell a lot of video game stuff. People come across them every once and awhile.
3) Any place where people are trying to sell used stuff and may not now the exact value of it, like yard sales, flee markets, Craigslist, etc.
Essentially, to get a WaveBird on the cheap, you're going to need to do some legwork and have some luck on your side.