My favorite zombie game is by far Zombotron 2. I love the graphics and it isn't too confusing or difficult. It is one of the few games that I have played many times over.
Sonny is one of my favorite games, but does it really qualify as a Zombie game? Sure, you play him, but there isn't much of a difference between you and the Humans. Plus, Zombies are usually about surviving against hoards and whatnot. The Last Stand series is my favorite.
Doesn't the main character die at the end? The boat runs out of fuel, in the middle of the sea.
He could... be picked up by another boat passing by on it's way towards another continent you know...
The question you are asking seems like an impossible one to answer for me, because my favorite game category is Zombie! Awww... well, if I really had to choose the ultimate, it would be... either The Last Stand 1, purely for being entirely awesome, timeless and plain fun, and Zombie Horde 3, because it has original day/night features, a LOT of ground to cover and explore and has a sure re-playability factor! =)