It's gonna be a rush if you visit Tokyo + somewhere else like Nikko, Fuji, Kyoto, etc.
Here's an example. Day 1 - Tokyo Disney (your pick Land or Sea). Both are huge, it'll take two hours of time just to get there and back from Tokyo, and the parks are large enough to gobble up a full day just riding rides. Expect 1-3 hour long lines....
Day 2 - Now, if you've got energy to rise early after Disney, get on the 6am trains (I'd say 5am, but with kids....), and head for the Fish Market. That'll take a good three hours just to navigate, but at least you get a nice fresh sushi breakfast at the local stalls around 9am.
After that, you can head over to Ginza (which is just two stops away on the train), and do some shopping and sightseeing of the area (you can spend days here depending on what you'd like to shop and do). Let's say see a major dept. store (one of three there that start with M). that'll take 3-4 hours to go through -- honestly! They're huge! And stop for lunch.
Next, you can check the local Ginza movie theaters and Kabuki for times later that evening.
Now, you can head off to Tokyo Tower and look at the skyline (since it's off the route of most major spots, it'll take it's own time). Another 3-4 hours gone there just to nav over, go up to the two decks.
You can now decide dinner there, or back to Ginza for some nice restaurants.
after, movie Japan-style, or Kabuki (do rent the English tapes!!! or else you'll never catch anything).
Afterwards, short break for ice cream, dessert, coffee at Detour Ginza, etc. then back to the hotel to rest and recover.
Day 3 - You still up for it? Maybe not unless you've been exercising and enjoy day long walks. Most people will start to feel pooped out by now, and their feet will hurt a bit (good walking shoes are recommended! forget the dressy shoes, go for the athletic shoes with good support!!)
Okay, off to see Ueno - huge park + museum - that'll take morning to lunch, easily. After that, a little shopping in the local stalls just south of Ueno station, then blast on over to the Imperial Palace. This is another long walk, so 2-3 hours just walking from one end to the other. I suggest north east entrance down to the south exit, then head over to Hibiya park.
Hibiya is a 1-2 hour walk, but nice and there's some very nice spots where it just looks gorgeous (north east exit overlooking the gardens).
At this point, probably good for dinner or a break, so zip over to Oazu or Tokyo Underground Mall and have a bite to eat (lots of food places underneath tokyo station in both the Tokyo Mall and Yaesu Mall areas). The passage between the Marunouchi line and the Yaesu side has three stories worth of eateries underground in the station walkway.
Now, it's darker, sun's setting, so great time to head on over to Shinjuku (if you don't mind the kids and sex shops), or Shibuya if you like more of a busy hangout for teens. I'd pick Shibuya over the two just because the homeless are quite common in Shinjuku, and the sex shops all over the place. (maybe not good for kids)
This can be fun as you can wander for ages around Shibuya, so 3-4 hours just shopping and walking.
day 4 - tired yet? Well, at this point, you can pick scenic things to do (eg. parks, temples) or shopping (Akihabara, Ginza, Marunouchi).
Temples are nice, so head on over to Asakusa - the biggest. There's enough to keep you occupied for hours, but by lunch, you should find a nice Okanomiyaki shop there to take a short break, or try a local restaurant. After, head on over to Sumida river and jump on the river boat rids for a nice view of the waterways.
Once you're off that, you can head on over to Meiji shrine. this one's a killer, so better have good walking shoes over the tiny rocks that line the way. 2-3 hours just to get into the Shrine center area, and back out again. Once that's done, head over to Takadashi dori nearby, and have a break.
Do that and walk Takadashi dori, sightsee and shop all of the young people shops there. Very unique.
By then, it's either a late break or dinner time, so you can eat around Takadashi, or somewhere else.
After dinner, you can head on over to an sky deck - Sunshine, Roppongi, etc. all have rooftop views of the city at night -- assuming you've done tokyo tower earlier in the day and want to see Tokyo by night. You can substitute a helicopter night ride here if you've got the money ($150+ per person for 20 min or so), or something else.
But likely be pooped after walking Asakusas + Meiji + takadashi, so back to the hotel.
Day 5 - if you love shopping for gadgets, Akihabara + Yodabashi is a MUSt see. Yodabashi dept. store is easily a 2-3 hour fast walk and just breeze through the many levels without stoppoing walk, or 4+ hours if you actually stop on every floor and check out every gadget and toy. But it does have a great toy store so worth stopping by just to bring back some fun things. Restaurants on the top floor are okay, but not special.
After Yodobashi, Akihabara exiting the JR station that's market so, and you'll see amazing sights. Basically, if you're facing the big buildings, just head right, then head right once you hit the main street. However, before you do this, the three or four tall buildings right in front are decent touristy gift places to pick up easy gifts w/o hunting around too much. This will take you north along the huge masses of shops there, and when you stop is basically when you run out of energy.
Otherwise, go up a few blocks and on the right will be a few food shops for a fast break - omisubiyo and takoyaki. Try the takoyakis if you're adventurous.
That done, Akihabara should have given you lots of tourist gifts.
At this time, it's up to you how to spend the rest of the Tokyo day before packing for home.
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Zipping over and spending a day at Nikko, or Fuji, or Kyoto?
You'll have to cut a day's worth out of the above, so you're pick.
If you zip out on two day trips (eg. Nikko + Fuji), then look into the rail pass you can buy outside Japan. It might be cheaper.
Basics? Shibuya, Asakusua, Tokyo Station underground mall, Tokyo Tower - That'll give you a taste of shopping, shrines, many foods, and a view of the city in a day - and these are mostly compact areas (everything closeby w/o walking around too much).
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