A good counter faction to Ninja-Zombies
I think that one of the best pairs to face ninja-zombies would actually be more unconventional. I have found that robot-wizards do extremely well against that match for a few reasons. The first is that they don't focus on killing your opponent's minions at all. This means that they focus entirely on their own thing and don't waste cards killing your opponent's zombies.
The second reason is that they build themselves up a lot. If your opponent manages to kill something (seeing stars), then you still have a base full of microbots and chronomages to score easily.The final reason is that ninja-zombies are very inconsistent. They cant draw as much and portions of their hand will always be useless. This makes cards like tech center and winds of change very useful because you can always have the cards you need.
I don't know what your preffered play-style is, but robot-wizards works very well against most factions. You just need to watch out for pirates and trickster because of base blocking and large removal cards.