Stick equal quality test barrels on a rail and actually test the rounds potential and I seriously doubt you'd see much, if any, differance in accuracy at pistol ranges (under 100 meters).
So many other things have a greater influence on accuracy than the caliber it isn't even funny. Barrel rifling, barrel length, action, shooter, powder type, bullet selection, bullet quality, etc . . .
I think a fairly accurate statement might be, "9mm hanguns tend (tend meaning more than half) to be more accurate than similar 40 S&W handguns (meaning identical designs in differant chamberings, IE Hi-Power, CZ-75, etc . . .)"
