There is no difference in boiling water from different methods. They all boil by transfer of heat into the system, causing increased motion of the molecules.

Electric kettle and pot on the stove both just use convection to heat it up. Microwaves use electromagnetic radiation to transfer the energy and heat it up.

The differences may be due to people using these different containers for things OTHER than water, and then not properly cleaning them out. Or it could be metals/minerals in the containers.

But no, the water itself is the same. It boils at 100°C (+/- based on air pressure, but generally)