For Pre-check they don't care about your choice of footwear. However.... if there's any supporting metal in the boots (e.g. an arch support or steel toe) it's going to set of the magnetometer, and you'll be asked to remove them and run them thru the x-ray. Depending on the boots, the eyelets for lacing them up might be enough to set off a sensitive mag.
Crocs and Sketchers slip-ons have been my new airport shoes of choice. No metal.