Public transportation is so abundant in central Tokyo, so you can easily spend your entire stay here without the need of using taxis.
But of course on a rainy day, or when you feel you have done enough walking for the day, you'll have no problems finding one close by.
Most taxis in Tokyo are small Toyota sedans that look like a model from the 1970s. They are actually much newer, but it seems the exterior has changed little in 40 years!
Some points to keep in mind:
・The doors in the back open and shut automatically! Only in Japan!
・Taxis now widely accept credit cards, but make sure to check if you are without Japanese cash.
・The driver may not have small change, so it's worth having a few 1000 yen bills in your wallet.
・Don't expect the driver to speak any English but by writing a memo of where you want to go, communications should be ok.
It's always handy to carry the hotel name card to show to your driver.
・Max pax number is 4. The trunk will only fit two suitcases.
・There is a 20% surcharge from 10pm-5am.
Vehicles are all maintained to a high standard and run on the meter, so there are no worries of being cheated. The only (but major) problem is that they tend to be expensive. A ride across town from Shinjuku to Tokyo Station will cost around 3,000 yen. From Narita Airport to central Tokyo will cost more than 20,000 yen!
Unlike other cities around the globe, Uber does not have a large fleet in Tokyo, because of heavy regulations and the fact existing taxis all run on a high standard. In Tokyo, Uber has simply teamed up with another taxi/limousine company, so the service you will be getting is not any different, other than the convenience of booking and paying through the app.
The only advantage is you are traveling with a larger group or luggage, but don't want to split into two vehicles, Uber has a fleet of Alphard or Hi-Ace type vans.
They also don't have the 20% surcharge taxi companies charge between 10pm-5am.
But again, because of Uber's small fleet, you might it easier to catch a taxi on the street as they are in larger numbers.