I'm thinking Infamous will be the better game. Its an exclusive, its made by the Sly Cooper guys (those were great games!), etc.
Since Prototype is crossplat, I have to wonder if Radical is contemplating the competition from Infamous, and putting more effort into their PS3 engine, possibly making the PS3 version of Prototype really cool, or if they will back down from direct compeition, and focus on the 360, and make the PS3 version merely "about the same".
Exclusivity has a tendancy to tip the scales a bunch, especially since Sucker Punch, like Insomniac, is a long-time PS-exclusive devstudio. Infamous for the win.