After doing more testing with the old IR thermometer (MLX90614) and re-reading the data sheet Ive realized that it isn't appropriate because the field of view (FOV) is too wide. Since our target is very small we need a thermometer with a smaller FOV in order to get a more accurate reading. This seems like a very good option. Let's buy it ASAP.
http://www.futureelectronics.com/en/technologies/semiconductors/analog/sensors/temperature/Pages/4099248-MLX90614ESF-ACF-TU.aspx
MLX90614ESF-ACF-TU
Francisco
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