The 047AN05 FCS chip is definitely the key, I couldn't get an S rank until I used it. Beef up your EN output, lighten your mech as much as possible, tune your boosters to get the most out of them, and with the 047AN05 chip you should get a good radar outlay of the map.
When the last wave of 4 subs surface, they'll make a square on the radar (one at each corner) Try to hover in the middle of this and you shouldn't have to move much to be able to lock on to each with two OGOTOs (or high powered sniper rifles, if you prefer) Just turn to face each one from this position, only move as close as you need to lock on, fire and quickly turn to the next. Firing two OGOTOs at once should be more than enough to sink each sub from this distance, so you don't have to wait until they've hit before attacking the next one.
I finished the mission at 177s this way, I hope it helps