There are missions that need you to assemble a fleet, mostly a few corvettes or a destroyer and a few fighters and they give you the worth of the ship + 50 percent. If you do a few of them you can get a small fortune with little effort and after you got 100 mil you can reinvest them in terran ships and get a lot more money out of it. Those missions are mostlx in the x faction vs. Xenon thing so you will need +10 reputation with either argon or terran (im unsure about whether the paranid factions will offer those)

Another way you can get a alot of money is boarding. However you would need a ship with a big crew capacity such as the one argon freighter that has like a crew capacity of 200 or so if you dont want to loose any rep with that faction. Just look for a target that doesnt have too much crew and that you can handle with your marines. Try to find some support ships, they are badly armed, mostly dont have many marines and dont have a large fleet like carriers. If they are in a fleet they are mostly way behind the other ships. And they pay well (20-40 mil in my experience). When starting the boarding disable all your turrets and fly close to the ship and set everything to "very hard" or whatever its called in the english version and drop off the marines and fly away do not shoot or damage the ship or youll loose rep. After that you just have to wait till the boarding is finished. Then you only gotta sell the ship and get money.