Hello....are you a Indian Tracker? ..with your ear to the ground? I'm kidding...its funny because I think we have all done this before!
I recently had my ear to the wall tracking a uninvited mouse in my wall. That little bugger drove me crazy! OK back to your question...
Well, hard to answer, try process elimination. Turn furnace off for a while, see if you hear it while running water from water heater. Maybe run furnace without anything else. It could just be the warm air in your heat ducts, they tend to bang some times. I actually have a very large unit in my house, (over kill) and it bangs sometimes because of the force it is providing. So..it is hard to say, can you go down stairs where the units are and trace the sound to its point? Hope this helps