Hi !
I do need an advice about the best way to travel in Tokyo : is it worth to take the JR pass or is it better to take the 72 hours metro pass ?
[We will be arriving on the 12/10 to Narita for a 4 days in Tokyo including 1 day trip to Nikko, We were thinking to take the JRpass for 2 weeks starting on the 17/10 as we plan on that day to take a train from Shinkonju to Matzumoto and continue to Kyoto Nara Myajima Hiroshima and back to Tokyo. But we could also take a 21 days to cover our stay in Tokyo if you think it is worthwile.. Many thanks for your advice
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For travel inside Tokyo, consider the 2-3 day subway pass:
http://www.tokyometro.jp/en/ticket/value/travel/index.html#anc03
For Kyoto, there is a good 500 yen bus day pass. Same thing for Nara, but most of the best places are in the Nara Park area.
For Hiroshima City, there is a loop bus that you can use with the JR Pass, and of course also on the JR ferry to Miyajima.
You can see some previews of many places you plan to see on:
https://www.youtube.com/user/thejapanfaq/videos
If you have time, just a bit past Miyajima is Iwakuni with its iconic historical bridge and mountaintop castle. Seeing Himeji is also worthwhile, and after a day in Kyoto, you can also go spend the evening in Osaka or Kobe.
If you don't use the pass to go to/from Narita, try the 1000 yen bus for a cheap transport.
http://accessnarita.jp/en/home/
You don't really need a subway pass to get around in Tokyo, unless you've determined that it works out for your sightseeing itinerary.
Though I do recommend getting IC cards (Suica or Pasmo) for each one of you, so you don't concern yourself with tickets and fare calculation.
http://www.japan-guide.com/e/e2359_003.html