How do you make money as a farmer?

Upgrade to max your bank and get the heroes who specialized to produce money like the resistance leader, the accountant and the orange hero the musketeer prioritize their skill production per hour and bank improvement skill. max them as possible.

Agreed, do all that to maximise your bank output.

Also try to complete as many event challenges as you can. The daily (hourly) challenges and Clash of Zones challenges and anything else that rewards money in chests. These give you the Stock items that contain resources and money which you can save up until you need them.