Tokyo is as great city. I was there for the Tokyo show... it is crazy and crowded(this coming from someone living in NY), but cleaner and more civilized than US cities of a similar size and surprisingly reasonably priced (as long as you are not expecting a large hotel room). I stayed near Shimbashi (also spelled Shinbashi), which is easy to get to from both airports and close to Tokyo station.
Honestly, JR is the best way to get around. Driving is slow, lanes are very narrow and parking is very tight. I would recommend getting one of the passes (which are offered at a discount to foreigners). We got a Kanto area pass, which lets you take JR rail trains and some of the slower (~180 mph) Shinkasen in the surrounding area for ~$80 for 3 days.
http://www.jreast.co.jp/e/pass/index.html
http://www.jreast.co.jp/e/kantoareapass/index.html
There is a Nissan showroom in Ginza, near the Ginza Lion (small, but the oldest beer hall in Tokyo). Sony HQ is down the street.
Yokohama is about a 40 minute train ride away. Nissan Global HQ is near the main train station and they have some exhibits and cars there. It is in a nice area to walk around near the water.
The NISMO Omori factory (which I didn't make it to due to time) is a little closer to Tokyo
http://www.nismo.co.jp/shop/shop/omori/ ... ex_en.html
http://www.nismo.co.jp/en/index.html
The Yokohama plant and engine museum are also nearby, but the engine museum is relatively small and the plant tours are only in Japanese.
http://www.nissan-global.com/JP/PLANT/H ... KOHAMA.pdf
Not about cars, but the Tsukiji fish market is also pretty cool to see. Sushi inside the market and right outside (a little cheaper) is about as fresh as you can get.
... And if you get a chance to make it to one of their industrial or science museums, take a look at one of their "kids" exhibits, strip away the cartoon characters, and you will be amazed at how advanced kids are over there.