Coyote is definitely the best bet, not because it produces the most profit, but because its the highest of those below that doesn't require daily management. Apollos make a fortune by selling the planes. If you go max workshops with 1 hanger, you'd be making over $3 million per base per month, but you'd be resetting the crafting every 8 in game hours (too tedious). The same setup with Coyote would produce over $1 million a month but would only require management once every 45 days.
If you do the math, I have to click 360 times more to achieve a couple million more per month, I'm sticking with Coyote armor.
I played one game doing Apollos and had 8 bases doing it making $24 million a month, had to make a macro for mouse movement and clicks which I would hit F10 every little bit to sell off the planes and start building more, just so my hands wouldn't hurt. After a couple months, what are you going to do with the cash...nothing that expensive in game.
With upgraded base facilities the profit per man day is as follows:
Apollo $1250 ($34583 per 30 days after expenses)
Jackal $320 ($6683 per 30 days after expenses)
Coyote $503 ($12177 per 30 days after expenses)
Alloys $200 ($3083 per 30 days after expenses)
Zephyr & Thunderbolt $333 ($7083 per 30 days after expenses)
Enforcer & Warhawk $250 ($4583 per 30 days after expenses)
Dual Warhawk $273 ($5265 per 30 days after expenses)