Do you run 87 octane or higher? Run the tank low and then put in a 91 or higher octane gas and see if it still happens. If it is an exhaust leak I would think you'd still get some popping. If you don't, could be plugs or carb set up.
Also... check to make sure all four cylinders are firing. Each pipe should be the same temperature coming out of the cylinders. Maybe one isn't firing right?
Cheap thing to try is Seafoam. Run the tank low (below 1/4 tank), pour in a full can of Seafoam at home, ride to a gas station 5 to 10 miles from home running off the main tank, and then top up the tank.