If you stay in Tokyo more than 2 days, I strongly recommend you to get IC card.
You can charge money to the IC card and use it almost every time you take trains and metros. It is very easy. You just touch it when you go through a ticket gate. You can check the balance in a screen at the gate.
You can save time because you do not need to check stations and how much it takes and line up for getting tickets.
The most reccomended IC card you can get in Tokyo is "Pasmo" .
Even in Nagoya, Osaka, Kyoto, and some other areas, you can often use the card (some train companies do not accept so please check details on the website or just try touching and see if it works)
Where : in major Metro stations
How to get : at Ticket Vending Machines (for kids, you need to go to office with your passport)
Price: deposit is 500 yen
Charge: 1000 yen - 10,000 yen
Refund fee: FREE (if you use Suica IC card from JR, you need some refund fee at some conditions)
In addition to trains, you can also use it at some Convenience stores, coin lockers, and drink vending machines!
for more information >>> http://www.pasmo.co.jp/en/use/