Ah hah! Found it.
You need to get 180 seconds or under for S rank. What I did... is dual grenade launchers on my back, quad precision legs (for sniping), and 2 050ANSR Sniper Rifles. And don't forget the 047AN05 FCS chip. Just try to find a point in the map where you have a clear line of sight to the subs and blow them out of the water. The speed at which you destroy the first 2 waves is unimportant, but destroy the last wave (the one of 4) ASAP!