Technically Samus could just freeze the Chief with her icebeam or a diffusion missile (Guided missles, that "penetrate all armor and shields"). She could cloak, plant mines, fly into him, whatever. She's got quite the arsenel in such a compact suit.
And Master Chief has, um... guns. Lots of guns. And I suppose a well aimed sniper round in the visor could take down Samus just as well. (It happens a lot actually, online multiplayer in "Hunters"). And although Samus's missils are mad to go through anything, maybe those new grenades in Halo 3 that make a shield could do something.
It's an endless struggle, and it's been debated before. I'm going to have to go with Samus, however. Chief couldn't avoid getting frozen solid. Take away Samus's ice beam and diffusion missils, it'd be a lot more evenly matched, though.
And Samus has done lots, storyline wise. She kills pirates, yes, but she's more of a mercenary. She kills off the hunters in the DS game to defend the galaxy from a doomsday weapon, she killed off the metroids themselves, cleansed infested stations and whole worlds, uncovered the secrets of a dead race (getting her suit as the result), and has the brief appearance as a researcher.
I dunno, I'm just more biased to Ms. Aran, as she seems a whole lot more.. human, then Master Chief.
EDIT: dug this pic off of my old HD.