Cabs are everywhere in Tokyo and Kyoto. At stations and major attractions there will be a queue of them waiting at or near the location, as well as near large hotels. They can be flagged down but it is just as easy to go to the closest stand and get one there. If at your hotel, look to see if there are cabs in front. If not, just have the front desk call for one. It will only take a minute.

An exception to the above might be at peak times or very late at night.