You can make a good argument that Master Chief is a bigger bad-ass than Samus and a better soldier and in many ways more terrifying, but Samus doesn't even operate according to the same laws of physics.
All of her powers are extremely radical and videogame-rooted.
Master Chief's own power armor is relatively hard sci-fi.
It's very difficult for hard sci-fi to win out over video game lunacy. Samus would win this fight.