In Tokyo? Everywhere: restaurants, hotels, bars, shopping malls, etc. as someone else mentioned, you'll only find squat toilets in older train stations, schools and probably older houses. read more
Seriously, Japanese style toilets are pretty hard to find in Tokyo these days. The only places where you might be hard pressed to find western style toilets are train stations and public restrooms in parks but even that is changing now. read more
Traditionally, most Japanese toilets were Asian squat toilets. These are still found in Japan today (about 10% of toilets). Asian squat toilets can be a bit tricky (and physically challenging) to use when you're not accustomed to them. read more
I don't think you will have any difficulty finding a toilet during your travel in Tokyo, BUT using a Japanese Style Toilet is a little different than the most public toilet in North America. In some parts of Southern Europe they have similar toilets. The majority of toilets in Tokyo are western in style. read more