In the head would be the best but I don't think it would make much difference if you hit him in the body.

HEAD SHOT

hen going squirrel hunting with an air rifle, there are several tips you should keep in mind. First, make sure that your airgun uses ammunition of a caliber high enough to be fatal. Many people make the mistake of trying to go squirrel hunting with an air-powered pistol. These airguns usually do not have enough power to be effective sporting tools, unless you can somehow get close to your prey (not likely with a squirrel). You need an air rifle that produces muzzle velocities in the 800-1200 fps range if you are serious about killing small varmints at medium to long distances.

Squirrel hunting is a sport of patience. Many hunters shoot the animals by staying in one place (usually around a food source) for an extended period. Eventually, the arboreal animals will come out of hiding and go about their daily business. If these varmints are startled, they will often hold perfectly still, flattening themselves again a tree. If you have a keen eye, this is the ideal opportunity to pick one off with your air rifle.
Squirrel hunting with an air rifle

Squirrel hunting is best done with an air rifle because all but the smallest caliber bullet rifles are just too powerful for the task. Many sportsmen prefer .22 caliber airguns. You can outfit it with a scope for more accuracy at distance.

Squirrel hunting is not difficult if you know where to look and the best times of the year. These animals are usually in abundance in dens they build in the tops of trees. They also like to make homes out of holes in large trees. Because these animals like to be as near as possible to a food source, look in trees near hickory nuts, acorns, walnuts, and bird seed. Once you find them, the air rifle will do the rest of the work.

If you end up merely harming the animal while squirrel hunting, be humane and end its misery quickly. It's inevitable for even the most accurate and experienced of hunters that shots will occasionally be a bit off target. This is especially true while using a lower velocity air rifle at a longer distance and/or into a stiff breeze.