Tokyo Metro and Toei have teamed up to offer a subway pass for tourists that can save you some yen, as well as being super convenient. Be mindful that the Tokyo subway lines are not operated by Japan Rail (JR) so you cannot use a JR Pass.
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What's the best alternative to the JR Pass? The best alternative is most likely a single-journey Shinkansen ticket. One-way or round-trip bullet train tickets are best for trips between popular cities like Tokyo, Osaka, and Hiroshima.
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.
For a limited time only, you can buy a Japan Rail Pass from certain train stations and airports in Japan. Travelers should be aware it is more expensive to buy a JR Pass in Japan than to purchase the pass online.
The JR pass is only worth it if you travel through different cities, if you are just travelling to Tokyo to Kyoto for example, I would just pay on the Suica. You can do the online calculator or just use google to calculate which trip is easier - paying individually on Suica or getting a JR Pass.
To be fair, most lines aren't that crowded most of the time. There are some lines that are a crush in the morning rush and if you want to avoid the crush you travel earlier (or a lot later). Making trains longer means you have to make stations longer.
Shinkansen is designed for high-speed train operation. There is no train crossings and have less stations than Conventional line for the high speed operation. The fare system is also different from other JR trains. You must have both the base fare ticket and the Shinkansen ticket.
While the metro lines do no accept the JR Pass, other IC Cards, such as the Pasmo and Suica, may be used. These cards give you access to almost any train or bus in Tokyo, and are a perfect complement to the JR Pass.
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.