I'm not sure from your question: are you trying to unscrew them from the outside of the casing?
If so you need to remove the nuts on the aft of the windlass aluminum cover, then slide the cover aft. You'll find a nut on the inside of the case on the switch. Remove the wires first, then the nut. Make sure you use a good sealant that you can get apart later to make the switches watertight to the case.
If the rubber boot you mention is the surface you press on, it has a lip that goes under the actual hard plastic switch that lies beneath. You'll have to remove the switch to replace that.
On my SM this is the proceedure for the Lofrans Tigres, but on older models it might be different.