In the last few years, GaN FinFETs are being considered as promising candidates for lower voltage applications over conventional HEMT devices. At the same time, GaN-based devices can operate in very low temperature environments that are relevant for superconducting and quantum computing applications. For example, due to its polarization-induced doping, GaN can overcome the carrier freeze-out challenges of other technologies such as doped silicon. This technology is not without problems, however. Structural inhomogeneity at the AlGaN/GaN hetero-interface, such as alloy clustering, becomes significant as the FinFET dimensions decrease. In this work, scattering rate due to alloy clustering is derived for Quasi-1D systems and added as an additional scattering mechanism in the in-house Monte Carlo transport kernel. Our simulation results show that alloy clustering limiting mobility is significant at lower temperatures. Therefore, any cryogenic analysis of GaN FinFETs must include the impact of alloy clustering.