What's the best APC formation for defense for the zombie siege/invasion event?

This depends on what you have available. Fighters - Vehicles - Shooters is a good general formation, but if you have heroes that favour one troop type or if you have a higher level of one troop type then you may want to prioritise them. There are also buffs for using all the same type of troops in an APC especially if you have completed research for each troop type or unlocked and upgraded the war room buildings.

Until you reach a level where you can easily complete all the waves you may want to try different setups to find what works best for you.