From just looking at just the statistics, I would have taken Emmitt Smith. From actually watching those two during the '90s, I would take Barry Sanders. I'm too young to have seen Jim Brown, OJ Simpson, Gale Sayers, etc. I saw Walter Payton at the tail end of his career. Barry Sanders played 7 or 8 years under Wayne Fontes. He had incredible numbers during that time, then you realize, this guy played in a pass-happy, run-and-shoot offense. He had NO FULLBACK those first several years. I think that's a big reason he got stopped for negative yardage so often. His first season with a fullback was under Bobby Ross. He gained 2,000 yards that season. He averaged more yards per run and more yards per catch over his career than Emmitt. He did it all with far less talent around him. I'm not saying Barry Sanders is the best RB of all time. He and his father have often said Jim Brown is the best back ever. Emmitt was a great back, but I'd have to rate Barry a cut above him.
You have it backwards. No one is faulting Smith for being on the team he was on. Everyone is praising how good a RB Barry Sanders was because of the team he wasn't on. I haven't seen anyone do the things Barry Sanders do on a team with no freaking offensive line. He was stopped for losses a lot simply because defenders were in the backfield before he got the ball. Speaks to his greatness that he still racked up those yards despite this. Stats and awards don't mean you are the best player. Take away the teams and compare them for what they are individually. Barry was a better RB.