How is the third battery wired with respect to the other batteries? Is it wired in parallel to one of the other batteries? If so,it should charge when that battery charges but if the isolater is bad, it won't.
How many banks (separate charging wires) does the boat's battery charger have? 1,2 or more)
Can you tell where the connections to the isolater go?
Is your issue something new or has it been like that since you got the boat?
If battery 3 were disconnected, is it only the sounder and plotter that won't run or are there other devices ( which I suspect) that are not powered.
The point is that is is difficult to troubleshoot without knowing what is what.