It is worth noting that you should be careful about heating water in the microwave. If you're using filtered water, and the container you're using is very smooth, it's possible to heat it beyond the boiling point, at which point agitating it can cause it to essentially explode. Ann Reardon talks about it in this video here, and like she also mentions in the video the U.S. FDA has warnings about it on their website here.

I clean my microwave once a month by using a cloth I've rinsed in hot water, and wrung out. If it's particularly grimy I use some mild soap too.