First, a list of potential Pokemon who could be very useful...
Charizard: He can fly for long periods of time and can protect you pretty well on land with attacks like Flamethrower/ hyper beam, etc. that don't even have to be near the targets. (Less chance of getting affected)
Pidgeot: Pidgeot could fly around for hours upon hours to bring you to safety.
Dugtrio: You could dig elaborate tunnels or even make an underground fortress so the zombies could never find you.
Alakazam: Why fight the zombies with physical attacks when you can ward them off with psychic abilities or create barriers to protect you. You would have to worry about running away, and even if you had to run away you can teleport to wherever you want.
Gengar: Similar to Alakazam except using ghost powers to infiltrate the zombies and take control.
Gyarados: Not much use on land, but if you chose to escape by sea he would do great.
Lapras: Similar to Gyarados, and you might even be more comfortable.
Dragonite: Similar to Charizard. Flying wherever you want, using long range attacks including fire, ice, electric, etc. Might even be a better choice than Charizard.
Steelix: Can dig elaborate tunnels and you wouldn't even have to worry about zombies biting him since he is pure steel. He could never get infected.
Scizor: Not sure if he is big enough to allow you to glide around on him, but he is very fast and could kill the zombies without them knowing what happened. Also, wouldn't have to worry about getting infected.
Wailord: You could jump in his stomach and wait things out under sea.
Flygon: Similar to charizard.
Salamence: Similar to Dragonite.
b]Braviary:[/b] Similar to Pidgeot.
Hydreigon: Similar to dragonite, except he has three heads. If one gets infected you just cut it off and still have two to go. lol
If I had to chose just one it would be
Alakazam without a doubt. (Mewtwo if we could pick legendaries) You could create endless barriers to protect you, control the zombies with psychic powers never having to get near them, and if they did somehow manage to get close you just teleport away. (Which beats flying, digging, surfing)