It'd be extremly close, Master Chief has been given extensive training since he was a child, about six or five years of age. However, Shepard, if I remember right, is part of the special forces of the Alliance (I think). Master Chief has been physically augmentated to a point where he could inflict a lot of damage to an average human being. Shepard, as far as I know, hasn't recieved physical augmentation. Master Chief wears a special set of armor, made out of a special alloy (I think) that includes energy shielding. Shepard, in meduim armor, lets say, has armor made out of a strong material, with energy shielding as well.So, in a hand-to-hand fight, alone against Shepard, Master Chief, in my opinion, would win.
Shepard wins with ease, because he is FREAKING AWESOME.That'll all that have to be said.