Steppers rarely go bad. Is this a Geckodrive G540 that you're using? If so, it has a spare driver. Making sure you shut everything down and let the capacitors drain before disconnecting anything, then switch the cables going to the Y axis so they're coming from the unused driver which is for running the A axis. See if the axis behaves any differently when you jog it (using the Home/End keys). If you've already used the A axis for a rotary table, disconnect it and connect to Y instead. If Y starts behaving better, you might have a bad driver, but that can be replaced.