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We are having a brief two night stopover on the way home (from round the world trip) in June 2010 and we may do a day trip to Mt Fuji and Lake Ashi on our only full day. Perhaps a dinner cruise the first night. We arrive 2.30pm on a Tuesday and fly out 8pm on the Thursday.
Can anyone suggest hotels/locations where we it would be convenient with transfers from airport and picking up tours?
Or, if anyone has a suggested itinerary for the time we would be there....happy to look at it. 
This will be just a brief taste of Japan and we'll probably be completey exhausted but perhaps we can go back another time for a longer holiday.
Thanks
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Two night stopover Tokyo - hotel suggestions please
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You need to deceide what you would like to see and how you want to spend the two days in Tokyo.
As for hotels, Tokyo is a big city, NRT is far from the city centre. There is a airport bus, (called limo) that picks up at various hotels and drops off at the airport or vv.
Since NRT is far from the city, you'll really only be able to spend the evening in the Tokyo on the day you arrive. At best, you have the morning and early afternoon to sightsee on the day you leave.
For accomodation, I'd look at hotels in Roppongi, Ikeburo and Shinjuku. I've stayed in all these areas on different trips, and I've never had a problem getting around by subway. I've also stayed in Ginza, but I wouldn't recommend it to a first time visitor.
How fun! My husband and I just returned from a 5 day trip to Tokyo. We stayed at the Hilton in Shinjuku. The reserved a shuttle bus/limousine service for us from and back to the airport. The shuttle was $30 each way.
The hotel was pretty convenient in terms of access to public transportation. We could walk to the Shinjuku station or we could take the free Hilton shuttle every 20 minutes.
Here are some pictures of the hotel from our stay. http://thepanthatcan.blogspot.com/2009/10/hilton-shinjuku-tokyo-japan.html
We were also able to arrange a halfday tour of the city at the hotel through Grayline. Our tour guide spoke English well and understood American humor so kept making jokes. Some other travelers on the half day tour with us also booked a full day Mt. Fuji tour at the hotel.
We were in Tokyo for the motor show so only spent a couple of days touring the city. On our first day, we woke up early, caught the 5:22am train from the train station closest to the Hilton on the Odeo Line to the fish market, watched the auction until 6:15 (when they close), bought some tuna and ramen for breakfast and returned to the hotel by 7:55 to take the tour. The tour took us to the Tokyo tower for a 360 view, the Meiji Shrine, and to the Imperial Palace. We were dropped off in Ginza for shopping and eating. The full day tour folks kept going.
Our next day in Tokyo, we ate ramen near the hotel for breakfast, went to Akihabara for electronics shopping, then to Harajuku to get a glimpse of the shrine and people watch. That evening, being Halloween, we went to a couple of bars/clubs and did some more people watching in Ropongi and Shibuya.
We spent the next two days doing motor show stuff.
On our last day, we hung out in Shibuya (the busiest intersection in the world) and then had robata in Shinjuku, people watched and went down the red light district like streets.
Have a great time!
The Oak Hotel in Ueno is very nice and is as convenient as it gets in Tokyo proper for getting to the airport--there are both an express train and a slower, cheaper one that leave from the Keisei Station that is nearby. The ride is about 50 minutes on the express and an hour and 10 minutes on the slower one. We paid about $80 USD/night for our room and really loved it there. It's also convenient to the Tokyo Metro and JR Ueno station for getting around the city.
Info and pics from our Tokyo stop on our own round the world trip at http://patrinadoestheglobe.blogspot.com/
Bon voyage!