[Hatix]

The JR Rail Pass is especially handy if you're going to use the Shinkansen a lot. Since you're going 2 weeks, and possibly a week in the south (Kyoto,...). you'll have to use the Shinkansen quite often, so it'll pay off. I also recommend a side trip to Nikko when you're staying in Tokyo (for which you'll have to use the shinkansen and a JR line, so it's all covered by the rail pass).
Also, it's a JR rail pass, so it's only valid for JR (Japan Railways). There are still many other railway & subway companies (like Toei, Tokyo Metro, Keisei, ...).

Going to Yokohama from Tokyo can be done in 2 ways. Take the Keihin-Tohoku line (which is cheap but slower), or the shinkansen (which is a bit more expensive and only 17 minutes from Tokyo station). But JR Rail Pass covers both .
And another tip, look for the english website of the shinkansen, and download the pdf with fares. And add them up to where you want to go (when using the shinkansen), and if it's worth it. It was worth it for my 2 weeks. I think I rode the Shinkansen about 12-14 times, and sometimes great distance, so it was worth it. The JR Rail Pass is only worth if you do great distances. And it's one pass per person.