Well Stewart hasn't played above A, so the safe pick would be Marte who had a pretty good year in AA. Bad BA but he was getting on base and slugging well. But for the potential... Stewart. He's better in the SAL then Marte was at the same age, and will be playing in Coors Field.
As for Helton vs Thome... Thome is a better hitter in real life. Better road OBA, better road SLG. That's why nobody is trying to trade for Helton and his ridiculous contract, and why Helton has recently said he doesn't want to leave Colorado.
"Jack, will you call me, if you're able?"
"I've got your phone number written, in the back of my Bible."