The problem is that your USB cable is acting as an antenna and picking up interference from your motors.
Large capacitors are useless in these situations as they only work at low frequencies and do nothing to remove high frequency interference from a motor. For this you need to use low value, like 0.1uF ceramic capacitors with very short leads.
These are needed across the motors as close to the motor power input as possible, as well as the power supply regulators input and output in parallel with the large capacitors you should have there.
If your motor only goes in one direction then you must have a reverse diode across it. If it can reverse then the driver must use four diodes to ensure there is always a reverse diode.
Also the layout of your wiring is very important and you should follow star wiring configuration, where all the grounds meet at one point. Keep all signal wires away from the motor and its wiring.