I can't decide. I have both. .40S&W and 45ACP (along with 357mag) are my preferred handgun calibers.
If I could have only one handgun caliber, I think I'd choose 10mm and learn to reload.
however, just between .40 and 45ACP, I'd choose .40S&W. I get an extra round. Stopping power is a wash except for trivial differences in theory and on paper. There seem to be more options as far as models of guns by various makers, especially in smaller guns most suitable for CCW.
I don't find one of the other better or worse to shoot. I prefer 165 or 155gr in .40 and 230gr in 45ACP. So comparing those, 45ACP has more recoil, but .40 is slightly more 'abrupt' and sharper (more like midweight 357mag).
Even the ammo cost is close, but 40S&W seems to go on sale more often.