The cards that always killed me when I ran zombies was:
Banisher of Radiance
Banisher of Light
Mystic Swordsman LV2
Basically, anyway you can kill their Pyramid Turtle or Giant Rats outside of battle, or keep them from hitting the graveyard will really hurt the deck's tempo. For the absolute best, I would focus on either the Banisher or Macro Cosmos, as Zombies are a deck really reliant on the graveyard.
What z4x0rz said, as long as u destroy the turtles outside of battle its all good, but keep an eye on vampire lord it can be hard to get rid off and they can always get him back with book of life (i hate that card lol)
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