I am no expert in noise, in fact I dont think anyone can really claim to have all the answers regarding it as there are just so many variables and what seems to work on one machine may make things worse on another. Industrial machines have for years used much higher signal voltages (24v) for normal I/O and differential signalling for smaller voltage signals (encoders, step/dri etc). That is the best approach but obviously it is not the easiest to implement on a system that is already built and set up.
The common sources of noise are VFD and Spindles, and other motors such as vacuum etc, finding which if any is the problem will just be a case of trying to run without and then introducing one at a time.
Hood