I think it depends on what you want/need because they offer two distinctly different skill sets. Pedroia will get on base better and more consistently throughout his career with his IsoD. Cano will hit for more power in every category. What do you want, more bases or less outs? There's a strong case for both.
I think Cano has a little better range, but he also has a stronger propensity for errors. And he suffers, IMO, from a lack of focus on the field, so some of his mistakes don't even make the scorebook. The stats all back Cano as a fielder, however. Tough call for me here. The same range vs. error issue exists between Gonzo and Lugo, and despite my mind insisting that you take the guy who gets to more balls, I can recall a few Lugo errors that have been game deciders. Yesterday was one. Sure, it happened in the first, but they are up 3-2, not tied w/o that run.