No expert here, but the Jeffrey's bark smells of vanilla or pineapple (honest, it's an easy way to tell them apart). Ponderosas smell resinous, if at all. My observation in California is the Jeffery seems to occupy higher elevations than the Ponderosa. Another way to differentiate them is grab a cone--the Ponderosa's will poke your hand while the Jeffrey's won't (spines are turned inward). Jeffrey cones are larger and heavier as well.

Jeffrey and sugar are probably my favorite Sierra pines.