Taxis are available pretty much everywhere in Tokyo.
Prices vary by region and operators, but typically typically the minimum price would be around 500 yen up to 1,096m, and 100 yen for each additional 255m.
Add 20% between 22:00 and 5:00. If you call a taxi by phone an additional charge will also apply.
For details, see the official page of the Tokyo Hire-Taxi Association: Tokyo Hire-Taxi Association
Getting on and off the Taxi
If you are one or two persons, you are supposed to sit in the rear seat. Otherwise, only one person can sit in the front seat.
The rear door is automatic and controlled by the driver, so never try to open of close it by yourself. The front door is not automatic.
If you have a large luggage, the driver will help you store them in the trunk.
Where and How to Catch a Taxi
If you are near a train station or an airport, it is likely that there is a designated taxi stand nearby. In that case, you will need to queue up at the stand, bcause they are not supposed stop at other spots.
If there are no taxi stands nearby, just raise your hand when you see a taxi. When the taxi stops by you and the rear door opens, get in and tell the driver your destination.
Japanese Phrases
These phrases may be useful when taking a taxi:
Kono nimotsu o toranku ni onegai shimasu. (Please store this luggage in the trunk.)
... made onegai shimasu. (Please take us to ...)
... made iidesu ka? (Can you take us to ...?)
Kono juusho made onegai shimasu. (Please take us to this address.)