Conker is a masterpiece IMO, my 2nd favorite game of all time, and probably THE funniest game I've ever played. I play it almost annually. I just absolutely love it. It plays out like a fantastic dirty cartoon, one that I could watch on a loop over and over and never get tired of.
Super Mario 64 is fantastic too, pretty damn close to being a masterpiece itself IMO. Level design was amazing, gameplay holds up VERY well today even if the camera is a little finnicky. Super Mario 64, though, was a SUPER important release for the company as well as gaming in general. It ushered in what a 3D game can be and do.
Both of them are amazing, 2 of my favorite games of all time, but I think Conker is the better game. Not by much though. One thing that just really hit home for me is that the way Conker disposes of the alien at the end is the same way Mario defeated Bowser in SM64...by grabbing him by the tail and swinging him around and tossing him away. I thought that the way Super Mario 64 ushered in the N64 and Conker was the N64's swan song... I just really loved that about the two games, like the N64 lifespan came full circle.