InFamous is currently the top dog of these two for me.
I'll be waiting to see both games in action before making my decision though.
The comparison is quite logical, both are super-powered open-world action games that were hatched from comic book inspiration. Though in the case of InFamous the comic books are mentioned expicitly by the developer and in the case of Prototype it is inferred by the Hulk game.
Extra kudos for the developer for mentioning DMZ as inspiration. More people need to read that book. Time for some plugging. Imagine this: A second American civil war has broken out (or the first American civil war, depending on your view) and the city of New York has ground both sides of the conflict to a halt. Manhattan is the agreed upon demilitarized zone and Matty Roth is sent in as an intern with a journalist crew to do a piece on the situation during a cease fire. Needless to say, Matty gets stuck and the war flares up again, leaving him to report on civilians who are forced to cope while the cannons roar far and close. Their country is at war, stores don't get supplied and paranoia has struck en-masse among the populace, but all the same, life still goes on.