I have no science to back this up, nor can I say it helps my chest freezer cycle less, but I have the thermistor in a foil bubble wrap and affix it to the side of the fermenter. Ideally, a thermowell could be used, but I don't use standard carboys for fermenting (I have 14 gallon plastic barrels for 10 gallon batches with a simple grommeted airlock).
YMMV, of course.