I've found the best method is to place a paper towel (the less "fluffy" the better...ala cheap/industrial paper towels) across the tracks just ahead of a locomotive and wet it with 91% rubbing alcohol (You'll want to avoid Goo Gone because it leaves a residue...alcohol leaves nothing behind).
While holding on to the locomotive, run it at full speed in the direction of the wet paper towel so that the wheels spin and run the truck nearest the paper towel onto it (Leave the other truck on the rails so that it can still pick up electricity).
Once all the black gunk is off that truck's wheels, stop the locomotive put the wet paper towel on the other side of the it. Then, reverse the locomotive's direction and do the same thing to the other truck.
Once this is done, repeat the process (both trucks) with a dry paper towel to dry off the wheels.
At
RITMRC, one of our members built a contraption to do this easier. Basically, it's a 2x4 with track on the narrow "side" with two rerailers spaced about 4 inches apart and a set of wires from each rail with alligator clips to connect to the layout. Each rerailer has some of the plastic cut away such that a strip of paper towel can be threaded over the rails and under the middle rerailer part. One rerailer is for the wet paper towel, the other is for the dry paper towel. It works great, it's portable, and you can do many locomotives in a row with ease.
If you're really interested, I can shoot and post some photos...
