Depends how big your motor is, if its a small one, less than a couple of amps a 0.1u cap accross the terminals, and one from each terminal to the case of the motor will quieten things down.
The noise could be comming from the controller itself if its a switcher, if its an industrial controller then there probably isnt a lot to worry about as it probably has filters on the speed inputs anyway.
You could try robbing a low esr 1000u cap from a scrap pc power supply and put it across the dc input if its powered from a dc supply,