Which one has a better recoil? How many bullets does each clip hold? What can you attach to these weapons? Do the differences between these weapons make one better-suited for one situation compared to the other?
The P99 holds fewer rounds (12 vs 16 for the Five-Seven) but does more damage per shot at close range (49 vs 36), although in practical terms this still means 3 body shots to kill a hostile with full life. The P99 fires faster. They both have the same attachments available. (Silencer, Akimbo, Tac Knife, Extended Mags). I don't have recoil statistics on them, but I believe they are both comparable.
The semi-auto clip-fed pistols are all pretty similar, so which one you choose is mostly a matter of personal preference. You might switch between them to gain the experience bonuses at various levels of use, but otherwise there's not really a huge difference.
If you want to compare other weapons in MW3, the chart linked from this question:
Modern Warfare 3: Weapon Damage Charts
is the best data currently available.
@Jo'nathanTummins, if you've got an answer you like, click the check mark under the number of the left to "accept" it, which shows other people that the question is answered.– agent86Apr 6, 2012 at 1:02