In practice, it's actually the opposite--the top layer readily loses its heat to the air, and the bottom is where the heat is being applied so it's hotter than the rest.
Generally as long as you aren't measuring in the top 1" or bottom 2" or so, the temps are going to read more or less the same throughout the liquid. Just don't get it too close to the surface, or too close to the heat source, and you'll be fine, give or take a couple degrees. There are strong convection currents that move the heat around throughout the liquid even before you get to a boil.
I take it you just want the thermo for monitoring your progess as you heat up strike water & sparge water, then later when you approach the boil, and finally to see when chilling is complete?
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