I'm shooting snowshoe hare rather than squirrels, but used to do a lot of squirrel hunting before moving to Alaska, and before taking up muzzleloaders.
In my own personal nutshell, anything but a head shot is a meat waster, no matter what I'm pointing. It's not just the actual tearing up of meat, but the spread of bloodshot well back down the body, even with neck shots.
In muzzleloaders I kind of hit the extremes in rounds while bypassing the calibers in the middle. I use 36, 32, and 30 cal in the smaller bores, as well as 50, 54, 58 and 62 caliber in the large. No experience with 40 and 45, but I can't make myself believe there's any special magic there.
I've also run the gamut of velocities, whacking them with full power loads in the big bores while on big game hunts, greatly reduced large bore loads, fast and flat small bore loads, and greatly reduced velocity small bore loads. They ALL do too much damage with anything but head shots.
Big considerations in picking a round are legal limits in some states, and for squirrel shots in trees, range or "carry" of balls beyond your target in populated areas.
Put it all in a pot and shake it real good, and you'll find what is best. I'm fascinated with 40 and 45 right now, mostly because I don't own them. But the up side of using my big bores is lots more field shooting and carry time, which has big payoffs when I move from small game to large.