For me, it would come down to Frank Gore vs. Larry Johnson, and I would go with Frank Gore.
Frank Gore's team is still improving, with Alex Smith still up and coming and the additions of Darrell Jackson and Ashley Lelie. While you may think this will lead to less opportunity for Gore, I think it leads to more scoring opportunities for him.
As for Larry Johnson, his team is on the decline. The quarterbacks on the roster have been ineffective and thus will have to rely on the run. Sure, this means that Johnson will still get LOTS of carries, but defenses will stack up against him. Let's not forget that he has had a lot of mileage in his few seasons as a starter. Running backs that rush for over 1800 yards in a season generally don't do well the next season.