There was a Mission Impossible game for the NES too - it was overhead view, based on the television series, and had you taking control of multiple agents to solve the missions. Rather interesting but it was not my cup of tea so to speak.
I know of the N64 game you are talking about, it looked interesting but I never played it. I may have to track a copy down one day.
If you get a chance to play one of the many variations of Impossible Mission then definitely try it out. It is a unique take on the action genre, mixing in lots of puzzle solving that doesn't slow the action down.
RE: Impossible Mission 3 Announced for Commodore 64