If this question was posed 5 or so years ago, I would have said without question, go with the .40, however there have been great strides made in beefing up the 9mm round without significantly bumping up the recoil (or pressues in the case of the +P), that I would have no hesitation recommending the M&Pc in 9mm for carry or home defense. The 9mm equates to higher capacity, lower recoil, quicker follow-up shots, and it's cheaper to shoot. And the cheaper to shoot, the more you shoot. The more you shoot, the more proficient you become. I keep my 9mm's loaded with the new Corbon DPX. It is an outstanding round with very impressive penetration and expansion qualities.
In short, the 9mm has come a long way in recent years and the reasons for going .40 are not quite as strong as they used to be.