There won't be much difference between the two as far as the guns are concerned (size, etc.). As noted, whatever you pick, get one that "fits"/feels comfortable to handle. Going to a local range, and trying out a few different makes/models is a really good idea. I like the Sigs - mine is a model 239, and it's available in both 9mm or 40S&W.

Generally, the 9mm will have less recoil. The 40S&W will likely be the better stopper as
it has a little more power, and uses heavier bullets. However, with good modern ammo
such as Federal Hydra-Shok or Remington Golden Saber, etc., either can be relied upon to do the job of stopping if you do your job - shooting accurately (center/upper torso hits).
Accuracy? - Well, that sort of depends on the shooter. Both are plenty accurate enough to be good defensive rounds. Heck, most encounters will be up close/personal anyway (within 10 to 20ft.).
As some have noted, the 45ACP is a good defensive round also, but it's a bit overated too. I know of a dog that took two rounds (185gr HP), and finally had to be put down with a 30/30. But, no matter the cartridge, we can all come up with exceptions for any
given cartridge. You get a hyped up perp, and it might seem as if it would take a bazooka to put him down. Sometimes only a shot to the central nervous system or brain will do. I like the idea, and practice for this also, of two to the torso, and one to the head. That ought to do!
In any case, whichever you pick, PRACTICE, PRACTICE, PRACTICE! Accuracy first - speed will come in time with more practice.