The lowest possible frequency such that audible noise is not an issue will result in least eddy current and noise levels.
Keep high impedance signals very short and avoid current loops, and stray LC coupling.
Make sure you have excellent grounds , shielding and CM ferrite filters where needed.
Probe using very short leads or just tip & barrel for signals < 50ns = Tr
I recall hearing portable power drills with motors in the early days around a few kHz, but many better designs now are silent.
If PWM is poor for noise and higher impedance when switch is off then consider going to full bridge VFD design with low impedance throughout mechanical cycle, but monitor current for limiting loading and changes in speed.