Is it safe to boil water in a microwave?
There is one very different issue to be kept in mind - water in a microwave can overheat and "explode" once it is disturbed.

Another poster had exactly this problem a short while ago: Water exploded in Microwave

So follow the usual precautions, e.g. putting a  wooden toothpick or a small, very clean stone (chemists have them in their labs) in your vessel. In a pinch, a spoon will do, but not all microwaves handle metal objects well.

If you are worried that heating your water in a microwave might not be sufficient to kill all "nasties", remember that killing bacteria is a function of time and temperature, so you might feel safer if you not only bring your water to a boil, but continue boiling it for another minute or so. I would assume that this is mostly for your psychological benefit, but it certainly won't hurt. The temperature reached is identical for different heating devices as physics dictates the boiling point of water and it can't exceed that as long as it's liquid.