Hulk no contest.
I am not familiar with any extended lore regarding Mr. Hyde, but from what I know he's just a more beastly and conniving human being, hardly what I'd consider to be overpowered. The Hulk on the other hand is one of the most physically strong and nigh invulnerable characters in the Marvel universe. Hulk would wreck Mr. Hyde, it would be like a High-School Karate star versing Mike Tyson.
Although, I do see the basis for this little contest, both the Hulk and Mr. Hyde have similar back stories and both are the transformations of two brilliant scientists. Perhaps if the question were, who is a better character, Hyde would stand more of a chance, but in a competition of physical strength, a fight, Hulk takes it.