This is actually a pretty interesting comparison when you consider that they both won a superbowl roughly around the same time in their career (Eli in his 4th year, Flacco in his 5th).
I think Flacco is a better QB now then Eli was in his 5th year, but right now...? That's a closer one than I initially thought. (originally had Eli by a comfortable margin)
I've never been much of a fan of Eli's but I won't discredit him, he's a legit QB with much better numbers than Flacco, but Eli also looked putrid last season.
I think I'd take Flacco beacuse of age. Plus I like his arm better. His ability to stretch the field with that cannon of an arm, combined with a solid offensive line is hard to beat. Especially if he's throwing down field to Dez... we would just be minus the solid offensive line.