family vacation in Tokyo in Dec

We are planning to be in Tokyo from December 27 to Jan 1 with our two kids 10 and 13 yrs old (4 of us total). We don't know what we should do and where we should stay to get the most out of these 5 days. We like to experience the bullet train and do shopping among other things.
Please help us plan our trip with tips that can help us get from places to places economically.

Are you flying in/out of Narita? Since the number of the days you have in Tokyo is so limited, it might help to also know the approximate arrival/departure time as well. It makes a difference whether you are flying in on the morning of 27th or in the evening :) And considering that it is in the middle of holiday season, I hope you already have accommodation booked. What are your interests?

You could use this itinerary suggestion function of this Japan Guide, though this does not give you a ride on Shinkansen:
http://www.japan-guide.com/e/e2400.html

Yes, we are flying to Narita (NRT). We get to Tokyo around 3pm on Saturday.

I currently have a reservation at Narita airport for 5 nights, but not sure if this the right way to go:
- Do you recommend we stay in downtown Tokyo- keep in mind we are 4, and I am having difficulty booking 1 room for four of us?
- Do we buy JR pass or simply take taxi from places to places in Tokyo, would that be more economical, especially if we intend to stay in Tokyo and the places of interest seem to be not too far apart?
- If we do book hotel in Tokyo, what is the best and economical way for us to get there from NRT airport?
Thanks again for you help.

Staying in Narita isn't a good idea at all as the daily ride by train takes at least 1 hour and cost as much for 1 person as 4 tickets for traveling around downtown Tokyo by transit. You could rent 2 twin rooms at a budget business hotel (check www.japanhotel.net), each room for 1 parent and one child. The hotel prices aren't that much different in Narita and Tokyo itself. On Arrival get a Suica-Nex combination (check the transportation section in A-Z at the very top of this site) this gives you a discount on travelling to downtown plus a rechargeable card to use on transit within Tokyo. The JR pass is only worth buying for long distance trips outside Tokyo. You definitely need to read that A-Z section!
Because of the language problems with taxi drivers plus crowded streets it is much easier to use public transit (Transit has signs in English). It is also a great experience if you aren't used to subways and trains in your home country. .

-Harajuku- great shopping and funky, vibrant fashion, good crepes!
-Meiji Shrine- very peaceful shrine, historical
-Shibuya- great shopping, restaurants famous busy crossing you see in movies
-Sensoji Temple- good souvenirs, historical temple
-Akihabara- electronics district, tons of gadgets and cool technology

Odaiba would be a cool and fun place for your 13-14 year old kids! Tons of amusement type places, and games arcades, very futuristic!

- I agree with everyone else - traveling between Narita and Tokyo costs at least 1,000 yen each way per person, and at least one hour each way. So yes, I recommend staying in Tokyo. Find either two twin rooms, each for one parent and a child, or try to get a larger room and ask for a sofa/extra bed or something. But if you have been having difficulty booking any room, keep the one you have for the time being as you search around.
- Do not buy JR Pass, since this is only good for really long-distance travel. Do not use taxis either, those are relatively expensive and the streets will be crowded. Get a subway and train map, and take subway or trains according to where you want to get to.
- If you book a hotel in Tokyo, and if upon arrival at Narita you buy the NEX-Suica combination ticket as suggested earlier, which gives you a very good discount, then you can take the Narita Express (NEX) into Tokyo. If not, the cheapest mode would be to take Keisei railway limited express (1,000 per person) - which is a commuter train - or the next economical option would be Keisei railway's airport limited express Skyliner (1,920 yen per person) - which is an airport-direct train for travelers (with space for luggage).

- For shopping, avoid late afternoon of Dec. 31st and Jan. 1st (of course) - things will be closed.
- Beginning with the hours close to midnight of Dec. 31st to Jan. 1st (and actually later), people go to shrines or temples to wish for a happy New Year (including Meiji Jingu Shrine and Sensoji Temple mentioned). Expect those places to be super-crowded. Super-crowded as in, if you are claustrophobia, avoid those places, and once you're stuck in it, you have no choice but to follow the very slow-moving crowd/queues.

- With such a short notice in advance it is somewhat difficult to plan any extensive traveling outside Tokyo - so you might not be able to experience the Shinkansen trains... you could take it from Tokyo to Shin-Yokohama (just a 20-minute ride, not going full-speed), but the price would be quite high for what you can experience.
- If you are into nature and also temples, you could take a day trip up to Nikko, or if you like zen-style temples, you could take a day trip to Kamakura (you can stay in Tokyo for the night). Considering that you are with two children, places suggested by tuti8a in central Tokyo may be better options.

Hi Syed. we just got back from a 2wks in Japan. We are a family of 4 too, Muslim, wif a 14yr and 9yr olds. Almost similar to you. We stayed at the Sakura Prince Tower in Shinagawa. Location very convenient. lots of choice for food. the family room is very spacious and luxurious @42000yen per nite. It is a bit pricey though but we will definitely return to the same hotel because of the fantastic service.

Since you are travelling with your kids, like us... maybe if you have the time.. make a trip to Nikko and visit the Edomura where it is a themedpark featuring the old edo era in Japan. Our kids really enjoyed their time there.. and unlike other westernised themedpark, it is very educational to learn more about the old Japan even for us. you can go to their website to check it out but please bear in mind to start early. (on shinkansen very fast but wif train transfers & kids you know right?) the journey took us 4hrs ... and the Edomura closed at 4pm.

We had a great time and the kids love it there too.

I like to thank you all for your sincere suggestions and tips. I feel much much better now. I cancelled the reservation in Narita and made new reservations at The Prince Park Tower Hotel. I will take NEX from NRT and will visit some your recommended places, I got similar recommendations from a Japanes co-worker as well. Shinkensen ride will be down at the bottom unfortunately this time. I also have added Edo Wonderland to my list.
Best regards.

for Edo Mura: http://www.edowonderland.net/nikko_e/access.html
From Ueno station in Tokyo (on the Yamanote loop line) to Nikko, using first a Shinkansen to Utsunomiya then a local train cost about yen 5430 per person one way. Cheaper trains take longer and with more change of trains. www.hyperdia.com give you fares, schedules etc. . read "help" first to enter variables properly.