That's another good question. I'd think Master Chief because I'd think that he is stronger and faster. I'd also think that Master Chief's armor is better, though that might not be true. After all, Boba's armor withstood the sarlac pit. I'd have to say that Boba Fett's bountyhunter gadgets and weapons are probably better than chief's. Boba might have more training because he was trained at a young age, just like master chief, but he trained with blasters, not throwing rocks at guards.
I'd have to say that Boba Fett would probably win. Even though Master Chief is unnaturally strong and has good armor, nobody knows how strong Boba's armor is, Boba is better equipped, has a jetpack for fast getaways, and just has better genes.