Accurate quantitative temperature measurements are difficult to achieve using focal-plane array sensors. This is due to reflections inside the instrument and the difficulty of calibrating a matrix of pixels as identical radiation thermometers. Size-of-source effect (SSE), which is the dependence of an infrared temperature measurement on the area surrounding the target area, is a major contributor to this problem and cannot be reduced using glare stops. Measurements are affected by power received from outside the field-of-view (FOV), leading to increased measurement uncertainty. In this work, we present a micromechanical systems (MEMS) mirror based scanning thermal imaging camera with reduced measurement uncertainty compared to focal-plane array based systems. We demonstrate our flexible imaging approach using a Si avalanche photodiode (APD), which utilises high internal gain to enable the measurement of lower target temperatures with an effective wavelength of 1 µm and compare results with a Si photodiode. We compare measurements from our APD thermal imaging instrument against a commercial bolometer based focal-plane array camera. Our scanning approach results in a reduction in SSE related temperature error by 66 °C for the measurement of a spatially uniform 800 °C target when the target aperture diameter is increased from 10 to 20 mm. We also find that our APD instrument is capable of measuring target temperatures below 700 °C, over these near infrared wavelengths, with D* related measurement uncertainty of ± 0.5 °C.