The easiest way to S Rank missions is to do them with a co-op partner. Make sure you and your partner are on separate teams. Have one person host the mission and have the other person register as a Mercenary. The host should find his partner in the "Merc pool" and hire him.
Go on the sortie and have the Merc complete as many subquests as possible, while the host hangs back and takes as little damage as possible. This will keep your income high and your repair costs & expenses low.
"Income" as well as "Repair Costs" & "Expenses", directly affects your overall rank. However, a Merc can take as much damage as possible without affecting any of it.
If you were both on the same team, income would be split 50/50 and it becomes almost impossible to S rank anything.