I'd love to say Boba would win, but in the end, I'm not completely sure. Master Chief has performed many individual acts that were immensely powerful, impressive, etc., and has a fearsome reputation. Yet Boba Fett is one of the most powerful men in the galaxy, and certainly the most powerful non-Force user. If anything, he seems to view the Force as a crutch; yet he understands it enough to basically be immune to most of its effects. That uncanny ability to simply not be intimidated by anything, including such "weapons" as the Force, accounts for a huge mental advantage for Boba. While Master Chief may be stronger or have greater engineered abilities, and the shield is a huge advantage, Boba still has the edge, mentally. I can't imagine that anyone, even Master Chief, could actually outwit our favorite Mandalorian.
Another thing to understand in such a fight is the fact that the only elements of Boba's armor or weaponry that aren't actually feasible yet are his laser weapons, and having a compact jetpack that actually contains a functioning rocket; while most of Master Chief's load-out still falls within the realm of science fiction. Not that that would necessarily be an advantage in an imaginary duel anyway, but its certainly worth considering.