Note that the article seems to be talking about the tools used to build the game, not the game code itself. I'd guess this means things like texture editing, level design, and such.
"[... ] our tools were used to model the characters for Super Mario 64".
I bet SM64 was written in C++.
EDIT: ... and possibly large chunks of it in C, too, since the C++ compilers always seemed to lag several months behind the C compilers on new platforms, and SM64 was a launch title.
