On Cottontails, I mostly use a .22LR and naturally aim at the head. In fact, I've never known any other way and not sure I know how else to shoot one. ..
Now, Squirrels is a little different. Again, mostly taken by head shots. Now if the range is long enough for me to doubt my shot, I aim for the neck, chest or shoulder. If it's in the 50/50+ yrd. range, I always got for the chest or shoulder. ....
One location that I hunt, the landowner requests that I only use a shotgun, for squirrels. That's fine as the place usually has it's share of rabbits. I take my trusty 24, .22 over .20ga. and load the tope barrell with a .22-Short. This is one great combo ....
Be Safe !!!