Mario 64 is one of my favorite games of all time, and a big reason for this is the awesome level design. I know people have made Peach's castle already, but what about the rest of the game?
I think the Bowser obstacle-course levels would be particuarly fun to remake in Minecraft. They could be done 1:1 scale pretty convincingly as they're mostly made of chunks in the game. And at the top, the big circular platform and Bowser himself
Aside from that, there's the floating island/tower map (the one with the owl), wet/dry world (underground town included, and a few others that would be interesting to do.