I would definitely suggest shielded cable. If one side of the pot is connected to GND, then that terminal would be connected to the shield. If none of the pot terminals are at GND, then you need a three conductor cable with a shield.
From the picture, I would guess that your PWM chip is running as an analog oscillator with the frequency determined by the pot setting. Since the pot is part of the analog oscillator, its leads are sensitive to noise. Shielded cable, series inductors and ceramic by-pass capacitors are probably required.
In an analog system, moving this pot is not as easy as it appears. Any noise coupled into the pot terminals could cause secondary oscillations and glitches in the PWM output.