For me it is easily zeppelin but you can't really have a straight comparison between these two great bands. Beatles were pop music, yeah sure it could be called rock but it was very commercial and uniformly loved by the main stream.
Led zeppelin were at the time, a bit mental and more on the edge and at first more underground.
I think listening now in 2013 most of zeppelins music still sounds fresh where a lot of Beatles tracks now sound dated. Also except for zeppelins final album I find all their previous ones legendary where maybe for me only half the beatles albums were great.
There are many other legendary bands, like the stones but when ever there are these large votes it always seems to end up a close vote between zeppelin and the beatles.
Great that most of the top rock bands were British! Stones, zeppelin, Beatles, Sabbath etc etc.