Sounds like you need a different stepper drive with ultrasonic chop frequency so its not audible,
but oddly the TB6600 datasheet seems to imply its range of oscillation frequencies is 20kHz upwards.
Perhaps something is malfunctioning with the drive, or some sort of sub-harmonic oscillation is happening
making things audible, and perhaps hitting a resonant frequency of some of the motor windings...
Can you record the sound?