Close call between Mario 64 and BOTW but I don't think I'll ever feel the same things i felt when i first played Mario 64. Everything was to be discovered and was so different from what I experienced before.
To be a little provocative, BOTW is what every Ubisoft games (Far Cry 3, Assassin's Creed, Watch Dogs,...) with an Open Wolrd tried to achieve. BOTW is the best Ubisoft-like game ever made.
Don't get me wrong, I really loved it, played over 250 hours and it's the best game I played in years.
BOTW is innovative... for the Zelda franchise... SM64, on the other hand, was and still is a revolution leading to what 3D videogames are now.
So SM64 for innovation, History and memories