I would say the brain.
And not through the skull, but through the ear.
BUT I WOULD DO IT STANDING BEHIND THE COW'S HEAD, SO WHEN THE PROJECTILE ENTERS THE BRAIN, IT WOULD TRAVEL TOWARDS THE FRONT OF THE HEAD, INSTEAD OF BACWARDS, ENTERING THE NECK, AND POSSIBLE BRINGING BITS AND FRAGMENTS OF THE BRAIN INTO THE BODY. WE HAVE ALL HEARD ABOUT SPONGIFORM ILLNESSES, AND EVEN IF THE ANIMAL IS HEALTHY, EATING BRAIN MATTER FROM ANYTHING IS NOT GOOD. IT IS A SAFETY PRECAUTION, WE SHOULD ALL FOLLOW, AND DUBIOUS, I THINK YOU SHOULD TAKE THIS INTO ACCOUNT BEFORE YOU GO AHEAD AND SLAUGHTER IT.
It immediately puts the cow down and greatly reduces the chance of pain or unnecessary suffering. I read the "emergency euthanasia" site too, and it makes great sense, although the part about shooting into the skull is kind of tricky, especially with how rounds fired from a gun is unpredictable as to what it would do to the target. It is better to aim at the lower brain, right behind the ear of the animal.
Shots to the respiratory or cardiac areas will also be sufficient to humanely put down the animal, as hunters, especially ones using muzzleloaders, always aim for the section where the shoulders and ribs are.
HOWEVER, with a hollow point you wouldn't want to do that, since you are eating it afterwards, you wouldn't want fragments of the ribs to be imbedded into the meat.