It's very hard for me to choose between these two bands because there both amazing and talented. But I have to go with the Beatles, what they've done in so little time is simply outstanding. I also prefer more songs from the Beatles then Led Zeppelin.
I think comparing the two is a bit like comparing apples and oranges. The fathers of pop compared to the fathers of blues rock ... both made outstanding achievements and no modern band is thinkable without the influence of both.
But if I really have to chose, I'd say the Beatles were a tad more innovative.
Although I do enjoy some of the songs that the Beatles put together, I just never got into that era of rock that they ruled. To me they are to whiney, I feel that their musical talents when put up against other artists is lacking.
But I will say that The Beatles did in fact have some good songs. Funny thing is I'd much rather hear someone else Covering their songs though. For instance I love the Soundtrack to "Across the Universe" and can listen to the songs over and over and enjoy 'em. But hearing the same songs performed by the beatles and I wanna gauge my eyes out with blunt pencils.
Zeppelin wins by sheer replay-ability. I enjoy the music and can listen to it more than once and still enjoy it. Not so with the Beatles.