The dangers of giving microwaved water to plants were emphasized when an experiment conducted as part of a science fair by a student showed one plant thriving and another struggling to survive. The struggling plant received only microwaved water, while the thriving one received stovetop boiled water. The test showed that within nine days, the microwaved water killed one of the plants. In both cases, the water was cooled to room temperature before being given to the plants.
The question raised about the experiment focused on what container was used while boiling the water in the microwave. It turns out a plastic cup was used for the microwaved water. The stovetop water was heated in a pot. It appears that the microwaving of the water didn't kill the plant, but more likely the chemicals leached from the plastic into the water are what killed the plant.
To test out the container theory, a member of the urban-legend busting website Snopes.com conducted another experiment. The experimenter used the same non-plastic container to boil water in the microwave and boil water on the stove. In this experiment, all the plants thrived.
Unless your water is severely comprised in quality, giving your tomatoes water directly from the tap won't harm them. If you do choose to microwave your water before giving it to your tomatoes, heat it in a Pyrex cup, not plastic. Heating water in plastic allows harmful chemicals to leach into the plastic. The water also needs to be cooled to room temperature. Putting boiling water, whether from the stove or microwave, will kill your plants.