When I say best, I mean the best overall for conpleting several different types of missions. One hero might be good for a specific mission (Clip with Resupply), but would be really bad for other missions. Here is my list
Constructor: Base Kyle. Pretty much a necessity for doing high level missions. Even when he isn't the commander, I always have him in support.
Ninja: Stoneheart Farrah. Makes bows actually good and can easily wipe out hordes with the xenon, cloud burst, and vacuum tube bow
Soldier: Commando Spitfire and Diecast Jonesy. With happy holidays and supports with Going Commado perks, they will melt a shit ton of enemies.
Outlander: Cyberclops. Is good with all energy weapons, especially high fire rate ones. Has 3 damage abilities and makes Teddy even better than it already is with the energy damage