Growth rates and alloy composition of AlGaN grown by MOVPE is often very temperature dependent due to the presence of gas-phase parasitic chemical processes. These processes make wafer temperature measurement highly important, but in fact such measurements are very difficult because of substrate transparency in the nearIR (similar to 900 nm) where conventional pyrometers detect radiation. The transparency problem can be solved by using a mid-IR pyrometer operating at a wavelength (similar to 7500 nm) where sapphire is opaque. We employ a mid-IR pyrometer to measure the sapphire wafer temperature and simultaneously a near-IR pyrometer to measure wafer pocket temperature, while varying reactor pressure in both a N-2 and H-2 ambient. Near 1300 degrees C, as the reactor pressure is lowered from 300 Torr to 10 Torr the wafer temperature drops dramatically, and the AT between the pocket and wafer increases from -20 degrees C to -250 degrees C. Without the mid-IR pyrometer the large wafer temperature change with pressure would not have been noted. In order to explain this behavior we have developed a quasi-2D thermal model that includes a proper accounting of the pressure-dependent thermal contact resistance, and also accounts for sapphire optical transmission. The model and experimental results demonstrate that at most growth conditions the majority of the heat is transported from the wafer pocket to the wafer via gas conduction, in the free molecular flow limit. In this limit gas conductivity is independent of gap size but first order in pressure, and can quantitatively explain results from 20 to 300 Torr. Further analysis yields a measure of the thermal accommodation coefficients; alpha(H-2) =0.23, alpha(N-2) =0.50, which are in the range typically measured.