Both are sh*t companies, but the reasons differ. Two sensible approaches...
1) Get some 121 turbine time then lateral over to a better regional like Skywest or Horizon. If you want to do that, then base your decision on available domiciles; as a really junior FO living in or really near domicile is the only thing that can enhance your lifestyle. You won't be there long enough for anything else to matter (like pay or upgrade time).
2) Quick PIC: Go to mesa. Both mesa and eagle suck, but why suck in the right seat for 7+ years?
If you are thinking of actually STAYING at mesa or eagle for a long time, you need to seriously re-evaluate and refer to option (1).
BTW, I was in your exact situation a few years back...