Find a base of one of their enemies and kill them all until you're neutral with the junkers. To find the base, check the patrol paths.

Who are their enemies?

Hogosha, Xenos, House Corporations

I dont suggest siding with the junkers, cause when I did, everyone else seemed to hate me.

But if your a criminal trader its a good choice.

Hang around Detroit and kill Xenos until the Junkers go neutral.

In fact, kill Xenos until the Liberty Rogues go neutral because if you fight the Rogues around Junkers, the Junkers will side with the Rogues. Rogues are known to hang out at Rochester.

If you think you can handle it, go to Colorado and hang around Ouray Base. This is the primary Xenos base and you don't have to wait long for Xenos to show up. The added benefit is that no other hostiles hang around here unless the Bounty Hunters hate you.

- the First Evil

Killing Xenos is the best way to help your rep with everyone. Once you get neutral with the junkers you can get into Rochester base and bribe the Rogues. Then you can get into Buffalo Base and get their Dagger light fighter. Also the Mule freighter should be available at one of the Rogue's bases outside of New York. You could get this freighter early in the game and make about a million dollars with it on cargo runs in Liberty space. I've played the SP game through twice and I'm starting out again and am going to make a ton of money early in the game and get the Dagger with a full load of Scorpians. Then I'll make a special-named save game and start all of my future games there. The early missions are fairly boring, especially when you're trapped in the New York system, it's a good way to cut to the good parts with some excellent equipment.