a PASMO PASSPORT. This is a special IC card with privileges only available to overseas travelers who are visiting Japan. It can be used for train and bus travel in the Kanto area and all across the country where IC cards are accepted, and for electronic payments when shopping.
A Suica card is a card you load up for transport, you can use this card for all forms of transport and even at vending machines and lockers. It covers all lines and you just pay however much you want to load up into the card. YA JR Pass is a one off pass for tourists that you purchase.
Even if you have a JR Pass or other travel pass, an IC card is recommended because it can be used across transportation systems operated by many different transit companies, as well as for payment at convenience stores, restaurants, shops, vending machines, and other locations.
In addition to using your charged PASMO card to ride the subway or buses, you can use it to pay for items purchased at stores and vending machines. It can also be used for member shops of railways and buses nationwide where interoperability is offered.
How to use PASMO. Simply touch your PASMO to the reader on the ticket gate to ride the train. Simply touch your PASMO to the reader inside the bus to pay the fare. PASMO can be used for easy electronic payments so there is no need to count out coins.
The only difference between PASMO and SUICA is who sells them. SUICA is from JR East, and PASMO is from Tokyo-area non-JR rail operators, including Tokyo Metro and Toei Subway. Wherever you can use SUICA, you can use PASMO, and vice versa. Same with charging with new amounts.
The JAPAN RAIL PASS is not valid for any seats, reserved or non-reserved, on “NOZOMI” and “MIZUHO” trains on the Tokaido, Sanyo and Kyushu Shinkansen lines. (The pass holders must take “HIKARI,” “SAKURA,” “KODAMA,” or “TSUBAME” trains.)
If you calculate that your travel costs will be lower if you buy individual tickets for each journey, then it's not worth buying a JR Pass. However, if you take into account journeys on Shinkansen high-speed trains or other means of transport, the savings you make become substantial.
You may get some value from some day type passes, but not from a nationwide rail pass. (if you were going as far a Kyoto, it would be about breakeven for you). A JR pass is of no value if you're only going to be in Tokyo. If you plan to arrive at NRT - http://www.jreast.co.jp/e/suica-nex/ - is a good value.
An IC card can be used for almost any public transportation in Japan. Both JR and private railway companies use IC cards, subways use IC cards, and most buses accept IC cards. There are some buses in more rural areas that do not offer this payment method, but in larger cities they are widely used.