Per Speer Ballistics Table
.40 S&W Speer Gold Dot 155 Gr. 1200fps 496ft. lbs.(muzzle) 389(50yds.)
.357 Mag Speer Gold Dot 158 Gr. 1235fps 535ft. lbs.(muzzle) 444(50yds.)
Take 100 fps off the .357 or for that matter even 50fps. (for the barrel length) and I would have to say the nod goes to the .40 S&W
My .357 has a 6 inch so it wins. Size Matters
Fiocchi 125 Gr JSP and HP ammo both have a MV of 1650 FPS fired from a 4" barrel. I can find some watered down ammo to skew stats for any caliber. Speer Lawman ammo is always at the bottom of the heap. I avoid speer ammo like the plague.
Now...that's good info..I actually looked up a different brand. I had a suspicion they would be real close. Accuracy would go to the .40 with longer tube.
Considering that almost every article or book I have read advises shooters to use 125 gr HP ammo with a 357 mag that is a very poor comparison. 158 gr ammo is for target shooting and hunting. You can come up with all sorts of impractical loads for the 357 mag to make the 40 cal look good. But when used properly the 40 cal just isn't in the same ballpark as the 357 mag. You can compare a 357 sig to a 40 cal but not the time tested 357 mag.
Here is another tidbit of information:
For personal protection, the full power .357 Magnum is the most effective of all handgun calibers. According to the police shooting results research conducted by Marshall and Sanow and published in their seminal book Handgun Stopping Power, the various 125 grain JHP Magnum loads from the major manufacturers achieved "one shot stop" percentages of about 93%-97%. It just doesn't get any get any better than this. These loads drive a 125 grain bullet at a MV around 1450 fps and ME of 583 ft. lbs. http://www.chuckhawks.com/most_versatile_handgun.htm