You have to be careful when microwaving water. If the bowl is real smooth, it can't boil, becuase the bubbles have to have some kind of imperfection to form. So it just kind of builds up and explodes when you pull it out and disturb it some way. You can just stick like a bamboo stick in there or something to prevent that if your container is smooth.
I would think that you could sterilize the water, but it would still have to boil the same amount of time in the microwave. I think it would be easier on the stove.