Free space optical communications (FSOC) systems are a promising complement to existing wireless communications technologies. FSOC systems have many significant advantages over traditional radio frequency links, including high bandwidth, no spectrum licensing requirements, low-power consumption, small payloads, low probability of intercept, and greater immunity from interference or jamming. However, atmospheric turbulence (scintillation) imparts significant phase noise onto the laser beam, resulting in intensity fluctuations at the receiver. In order to develop scintillation mitigation strategies, it is necessary to monitor scintillation in parallel to the communications channel. We report on the development and implementation of a robust angle of arrival (AoA) turbulence measurement instrument that is suitable for this task. Several key data acquisition and processing techniques were designed to enhance the reliability and robustness of the scintillation measurement.