"where is the Flue located on a Goodman GMP100-3 furnace"

It is the vent pipe that hooks to the draft induced blower as far as I know. Don't hear it called a flue much these days. Can you let us know more about your situation? Actually, now that I think about it, I believe they may call the portion of the vent that is outside the "flue". Basically a vent termination.