Been through this on one boat. It was a windlass power issue. You probably didn't need a new motor, just a competent boat electrician. Corrosion can creep up inside the cable's insulating covering quite a long ways. Electricity flows over the surface of the strands of wire, not through them.This is why they must be clean for a good connection. Connections can look good, almost perfect and still fail. I use a brass brush that looks like a toothbrush to clean every terminal and use contact cleaner to help. They should look shiney once clean. I don't just clean the wire ends. I also clean the windlass and in your case the thruster connections. Change any fuses in the system and clean the contacts, same for circuit breakers. Corrosion can creep inside of them as well. Then check the power cables resistance with a multi meter to make sure they meet spec, if everything is still running poorly. I can't tell you what resistance is acceptable because I'm don't know the wire size or length of the runs for your equipment. I'm sure it can be looked up online.
Also, with both the thruster and windlass getting weak, that could be a sign of a battery bank with a few weak cells in the batteries. I would have them tested one at a time after a full charge. If that comes back OK, I would let them sit for 24 hours with nothing connected and have them tested again.
What a pain in the transom.