I'd guess that a microwave would "waste" more energy as it's got moving parts and the energy isn't completely directed to heating the water. A kettle also "wastes" some energy as you end up heating the kettle too (from the hot water).

If a microwave was more efficient, I'd expect to see premium kettles that used microwaves instead of a simple heating element, though maybe there'd be design problems with preventing leaking microwaves.