Hummmm, this is nothing like apples to apples and you haven't provided any info about your team. Still, this question interested me enough that I just put about 20 minutes into researching it for you, hehe.
Pedroia, 23, put the ball in play almost 94% of the time this season in AAA - his bat stays in the strike zone forever. He's from an adjacent city to where I'm living now, and is legendary for being one of those guys who never struckout in high school. I see this Arizona State grad as a slightly above average MLB 2B.
Iannetta, 23, was more known for his defense than bat entering this season, but that has changed. Not only did he rip the cover off the ball in AAA (they must not be using humidified balls yet for the Sky Sox), but the North Carolina graduate also walked almost as much as he struck out (24-29). Iannetta has had decent pop since college, but he has never hit as high as he did this year in AAA, .350. I see him as an above average catcher right now.
Really, these guys are pretty close. Right now, I have Pedroia as my #21 prospect going into 2007 and Iannetta at #39. I still have a lot of polish to put into my list, but given that both players are in the bigs to stay as of now and their 2006 mlb number of at bats probably won't be enough to put a lot of weight into, I think they'll remain pretty close for me. So, it all comes down to which above-average, but probably not All-Star caliber player, you want to roll the dice on.
Mike Pelfrey > Matt Garza