Except one is $1.29, is a single song, and was incredibly hyped up. The other is $16.99, an album, and was released spontaneously. Also, Gaga was still on the rise as a growing artist, while Beyonce is an established artist with a decade and a half under her belt and yet is still performing better than ever. This does not create Beyonce's "legacy" like Born This Way did, it simply reinforces what we all knew.
I have nothing against Gaga, but don't compare her to Bey in this respect. It just doesn't make sense.