Obtaining thermodynamic measurements using rotary-wing unmanned aircraft systems (rwUAS) requires several considerations for mitigating biases from the aircraft and its environment. In this study, we focus on how the method of temperature sensor integration can impact the quality of its measurements. To minimize non-environmental heat sources and prevent any contamination coming from the rwUAS body, two configurations with different sensor placements are proposed for comparison. The first configuration consists of a custom quadcopter with temperature and humidity sensors placed below the propellers for aspiration. The second configuration incorporates the same quadcopter design with sensors instead shielded inside of an L-duct and aspirated by a ducted fan. Additionally, an autopilot algorithm was developed for these platforms to face them into the wind during flight for kinematic wind estimations. This study will utilize in situ rwUAS observations validated against tower-mounted reference instruments to examine how measurements are influenced both by the different configurations as well as the ambient environment. Results indicate that both methods of integration are valid but the below-propeller configuration is more susceptible to errors from solar radiation and heat from the body of the rwUAS.