Using the Purdue University Airborne Laboratory for Atmospheric Research, we measured concentrations of methane and ethane emanating from seven U.S. cities (New York, NY, Philadelphia, PA, Washington, D.C./Baltimore, MD, Boston, MA, Chicago, IL, Richmond, VA, and Indianapolis, IN), in order to determine (with a median 95% CI of roughly 7%) the fraction of methane emissions attributable to natural gas (Thermogenic Methane Emission Ratio [TMER]), for both summer and winter months. New methodology is introduced to compute inflow concentrations and to accurately define the spatial domain of the sampling region, using upwind measurements coupled with Lagrangian trajectory modeling. We show discrepancies in inventory-estimated TMER from cities when the sample domain is defined using political boundaries versus urban centers encircled by the flight track and highlight this as a potential source of error common to top-down studies. We found that methane emissions of natural gas were greater than winter biogenic emissions for all cities except Richmond, where multiple landfills dominate. Biogenic emissions increased in summer, but natural gas remained important or dominant (20%–80%). National inventories should be updated to reflect the dominance of natural gas emissions for urban environments and to account for seasonal increases in biogenic methane in summer.