This is a fairly hidden location since you won’t pass by here through story missions or jobs. You can either discover this location on foot or after liberating the Jefferson Rail Tunnel Ambush Camp. Aside from its location, you also need to worry about a small Horde along the way since the mine is near the horde’s watering hole and feeding ground; not to mention that the mine itself is that horde’s Nest.
Once you cleared or pass by the Horde, simply enter the mine (during the evening if you’re trying to stay away from the horde) to find the Beacon inside, with the NERO Injector case.