Can't really say either one is better than the other since they're two entirely different games. Yoshi's Island along with DKC2 represents the pinnacle of 2D platfomers in the 16-bit era, while Mario 64 was the first game to fully realize 3D control and platforming gameplay.
Both are exceptional games that stand the test of time, but I guess you'd have to give the edge to Mario 64.
On 2/24/13, MB1025 said:
You know I was always wondering why no one ever used the dollar sign for $ony, but then I realized they have no money so it would be pointless.