To solve a noise issue you need to identify the source, the stepper motor electronics/wiring/stepper motor and the means of coupling, here you are assuming the common power supply, which sounds reasonable. But you need to test the theory, can you run the sensitive circuitry from say a battery? and does that eliminate the noise? There are lots of modes for noise at such a low level to couple, inductive, grounding, resistive, magnetic and electrostatic, you want to be sure you are fixing the actual cause.