My personal Party of pokémon to survive a Pokémon apocolypse would include;
Tropius
Magikarpx2
Rhydon
Chansey
Castform
Magikarp are Rapid breeders, able to produce a multitude of eggs. for proivded I can last on crops (hello Castform + Tropius) I will soon have a Magikarp Farm, fully equipped to service food worries. The Magikarp could also reach Gyarados level godlyness.
Chansey would be the healer of the team, just in case something goes wrong.
Castforms weather changing abilities would be paramount to me obtaining Water (to boil off and drink, plus to keep the crops ) and keeping the crops in suitable growing conditions, due to it's weather changing abilities. Tropius can also assist in a balanced diet (and pre-magikarp farm food) And would be an excellent escape option.
I was debating whether or not to choose Dugtrio, Excadrill or Rhydon in this last slot, but I went with Rhydon due to it's ability to Surf and drill immense holes in the ground, effectively creating a chasm for the zombies to fall into. Whilst Dugtrio can help with the fields, I feel having a secondary escape route across water was more important.
EDIT: Reread first post.
Rhydon would be my choice out of the six mentioned above. It provides me with incredible trap setting utillity (Hooray Chasms) + Surfing escape routes across water just prove too valuable to give up. Yes I'd have to find food and yes, flying types seem like a bettter choice but all pokémon get tired and Flying types generally can't do squat when you're foraging around a building seeking out supplies.