Our vacation will be in April 2017. Arriving at Narita Airport. Based hotel at Hilton Tokyo Bay to see Disneyland and Disney Sea for the last 2 days. Is it possible to have a day trip to Kyoto and Nara. We want to stay in a Ryokan where we can view Mt.Fuji and try the onsen. Where is the best place? is it in Hakone or at the Kawaguchi lake area?
About the Imperial Palace, Which is better to go on a tour, the one in Tokyo or Kyoto? We like sightseeing and we are a foodie people.
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I would discourage you from trying to do Kyoto and Nara as a day trip. In the very least it is worth an overnight and 2 days. One way by bullet train on a rail pass is 3 hours, and you'd have very little time to see much as a day trip.
Both Hakone and the Fuji 5 Lakes area have onsen. But the Hakone ones are more famous.
Since July, the Imperial Household Agency has removed its requirement of signing up and joining a tour. In Tokyo the East Gardens are something to go see, and there are 3 places in Kyoto. There is the Kyoto Imperial Palace, Shugakuin Imperial Villa and the Katsura Imperial Villa. The first is honestly not that interesting, but the latter 2 are much more beautiful.
For what to see, I suggest you look at:
http://www.gotokyo.org/en/index.html
http://www.japan-guide.com/e/e2164.html
http://www.kyoto.travel/
http://www.japan-guide.com/e/e2158.html
http://www.japan-guide.com/e/e2165.html
For food, try:
http://www.bento.com
How long is your stay in Japan?
Is it possible or better yet to stay overnight at Hakone and have a day trip going to Kyoto? How far is the travel time with the JR lines?
You could ask 5 different people what the best restaurant is and get 5 different answers. There are many factors - taste, price, portion size, service, etc.
You might look at these to get some ideas - I wouldn't lock yourself down to just one place or nothing, however.
http://en.rocketnews24.com/2015/01/28/lets-take-a-tour-of-the-best-sushi-in-tokyos-tsukiji-fish-market-with-mr-sato-part-1/
https://www.tripadvisor.com/RestaurantsNear-g1066444-d315477-The_Tsukiji_Market-Chuo_Tokyo_Tokyo_Prefecture_Kanto.html
Going to Kyoto from Hakone (Mishima Station) won't help you much - at best it will buy you one hour more, if you take the Hikari bullet train.
You can see regular fares, routes and schedules on Hyperdia.
http://www.hyperdia.com
Again, I suggest that if you want to see Kyoto, you do it as an overnight trip.