It looks to me like it's geocentric height:
https://github.com/brandon-rhodes/pyephem/blob/master/libastro-3.7.7/earthsat.c#L534
I've tweaked the docs to make this claim:
https://github.com/brandon-rhodes/pyephem/commit/990f2a26260f19dd679c932fe9f8a071505e88ff
Though, note that Earth satellite computations are often not accurate enough to make the difference between the two systems important, as they're regularly several kilometers off.
The newer astronomy library Skyfield has routines in its earthlib.py
that convert between geodetic coordinates and x,y,z vectors. If you did the math yourself for the conversion between x,y,z and geocentric coordinates, you could run a complete conversion between the two.