Try Preview. It's free, It has Instant Alpha PLUS a Smart Lasso that you can use to select the area you want to remove. Just perform the action you want (the options are under the "Select" toolbar object), press "Delete" to remove the selected area, then, when you Save as png, it automatically adds the Alpha channel.
Preview's limitation is that it will only let you perform Instant Alpha on a bitmap. Anything you copy from Keynote to Preview automatically gets converted to a PDF, so it's no go. You'll have to bring in the image from it's original location (on your HD for example) to Preview directly. If you don't have access to it, then it's a two step process. First, copy the image into Preview, then save as .png (since it's lossless), then open that png and apply Instant Alpha.