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:
is the best data currently available.