I've accidentally pushed my stopped into my carboy too far once, not enough to dunk it in but enough that it was flush with the top. Had a hell of a time getting it out. I wish I could offer a solution to the actually retrieving of said stopper, but wow I can't even fathom how to get that out once you've siphoned your beer out.
My sympathies, best of luck! And your beer will be fine, most likely, unless your stopper was previously used as a drain stopper in your bathtub