Before you get rid of them, you might want to make sure you don't have any of the rare ones. The rare ones can fetch over $400, and there's one that's supposedly worth more than $2,000.
[URL="http://en.allexperts.com/q/Beanie-Babies-2189/"]Beanie Babies[/URL] - from All Experts
You could also sell them in potluck lots on eBay starting at a set price that will cover postage.
But, if you are sure you want to donate them--and it's awesome if you do--why not look into charitable organizations like the Salvation Army? Or maybe a homeless shelter could use them? Or, if they are in mint condition, and you don't have to get rid of them right away, maybe Toys for Tots will take them off your hands next Christmas.
Just tossing out ideas to look into.