I will be arriving at NRT on Dec 25 around 9 a.m. and only have 48h in Japan.
I have just spent a week in Tokyo and this time I was thinking about going to Kyoto or Nikko. The only thing is that I need to get back to NRT on Dec 26 in the evening as I have to catch a flight at 11am on Dec 27.

Kyoto:
I know it's a bit mad to see it in such a short time but I could catch a NOZOMI from Tokyo station at 12 and be in Kyoto around 2.30 p.m then leave Kyoto on Dec 27 around 6.15 p.m and be in NRT late on that evening. Which hotel would you recommend for a such a short visit ? Granvia? Hyatt ? Okura? ANA?
Since it gets dark quite early which part of the city would you visit on my arrival day?

Nikko:
Seems like travelling time would be more or less the same whether I use the bus to Utsunomiya or by train via Asakusa. Is Nikko nice in December? would it be really cold ? Any nice hotels ( I like my comfort).

Thanks a lot for your input.

Nikko will be bitterly cold at that time of year; with daytime highs around freezing.

Kyoto can also be cold - but I'd suggest Kyoto rather than Nikko.

For Dec. 25, I'd suggest the Granvia. Staying at the station allows you to drop your bags and go straight out. And next morning you can leave bags with the concierge - ready to pick before catching the Shinkansen back to Tokyo.

Assuming you arrive in Kyoto around 2.30pm, you'll probably have time to see one thing before dark. You could make it to the Nijo castle, for example. Last admission is at 4pm and it's closed from Dec 26 through Jan 4, so that day is your only chance to see that particular place.

For the next day, you should pick an area to explore in depth. Best to check very carefully that the places you might want to visit will be open. If you want to cram the max into one day, you could get a very early start at the Kiyomizu dera.

For Dec 26, I'd suggest staying at a hotel near Tokyo Station. Either the Hotel Metropolitan Marunouchi or the Marunouchi Hotel (there are also cheaper business hotel options towards Nihonbashi).

Staying at one of those places makes it quite comfortable to use the last Shinkansen from Kyoto to Tokyo. That means you can enjoy dinner in Kyoto, catch the last train at around 9.30pm and arrive at Tokyo Station shortly before midnight. It's not bad when your bed is just a couple of minutes walk away.

And in the morning of Dec 27, you can easily catch the 7.30am or 8.00am N'EX to the airport.

And a very early start is recommended, it is the most popular spot in town, and the must-stop for first time visitors. However, as Mrs. Pickles says (quoting Yogi Berra), it is so crowded that nobody goes there anymore.

I was in Kyoto this weekend, and visited some really out of the way and seldom visited (but incredible) sights, which is what I always do, and the best way to really get into the atmosphere there.

Thx a lot Jib71. I didn't know that Nijo Castle was closing for 2 weeks. I really need to get to Kyoto as quickly as possible after landing in NRT.
I have a room paid for by my company in NRT and that's why I was thinking of going straight back to NRT on the 26. Do you think that leaving Kyoto around 6h30 pm and catch a late NEX or Skyliner to NRT would make such a huge difference in my enjoyment of the city considering the fact that it's getting dark early and that I would probably be dead tired?

Pickles. Thanks. So would you think that on a 1st visit I could skip some of the major sights and go for some less visited ones ? If yes what would you recommend ?

that's a quick trip to kyoto..but i think it's doable.

That's a tough call. Given that you have limited time, you should stick to one area of Kyoto, certainly. The easiest to get to from the station and the one with the highest concentration of sights is Higashiyama (Eastern Kyoto) which is where Kyomizudera is. You could easily spend a few days in Higashiyama itself, but the sight-of-sights there (you know, the one in the "if this is Tuesday it must be Kyoto" bus) is Kiyomizudera, for better or worse, the Eiffel Tower of Kyoto.

If you get there early enough in the morning, and given that it is December 25th, a regular workday in Japan and not high season (high season in Kyoto is the late fall and the late spring) it may be fine. There will be some crowds, but nothing like making line at the David in Florence. It definitely is worth seeing, but it isn't going to be the atmospheric Kyoto sight some people are looking for.

If I had one day in Kyoto I would get an early start and head to the bottom of the Kyomizuzaka slope (or take a taxi to the top of the slope) visit Kyomizudera, followed by a walk around the Kiyomizuzaka, moving along the Ninenzaka into Nenenomichi, stopping to check out the stores and a temple or two along the way, and walking all the way up to the Philosopher's path. In a leisurely walk, this could very easily take you a full day if you stick to visiting 2-3 temples in detail and a leisurely lunch somewhere atmospheric.

Another, much more "secret" experience is to take a taxi to Arashiyama in Western Kyoto, and walk from the Arashiyama center up into the Sagano hills all the way into Toriimoto. Lot less crowded and quintessential Kyoto.

There are many other 1-day rounds out there, but they involve some crazy transport to some out of the way places that not even the Japanese know about.

Thx for your invaluable help Pickles. What a shame I only have such a short period of time. Will look into your suggestions.

For such a short visit to Kyoto, you will need to plan your transportation/walking routes to make the best use of your time. Get a guidebook with maps and plan accordingly. Also, be sure to stop at the Tourist Information Center, either at the airport or on the 9th floor of the Kyoto Station building, for specific tourist maps and information. The TIC at Kyoto Station will also be able to advise you of any local closings or other problems. Kyoto Station, particularly from the top floor, is worth a photograph or two in itself.

In no particular order, but concentrating mostly on the east side (like Pickles, I think that is where you get the most bang-for-the-buck), I'd suggest:

Sanjusangendo Hall - just east of the station area and on the way to Higashiyama.

Kiyumizudera - the one "must do" but will be crowded even in December.

"Pottery Slope" and Sannenzaka - just north of Kiyumizudera.

Nazenji - a short walk further north.

Heian Jingu Shrine - should be pretty in winter. If there is snow (unlikely) it will be beautiful.

Ginkakuji (Silver Pavillion) - at the north end of the Philosopher's Path. If you walk the whole thing, this is where you come out. Might be easier to take a cab or bus.

Nijo Castle (Nijo-jo) - take a cab or subway to get across town. This is far better that the overrated Imperial Palace.

That is more than you can comfortably do in one day but if there is extra time, consider a cab to Kinkakuji (Golden Pavillion.) Ryoan-ji , with the famous Zen rock garden, is a short walk away.

Have a great visit.

You may have figured this out by now but the last Narita Express leaves Tokyo at 20.03 (and Shinagawa at 19.50), so you'll have to leave Kyoto at 17.16 or 17.23 in order to catch this train on 26th. It's unfortunate that you have to stay near NRT on the night of 26th. Since you are likely to be staying in Narita itself rather than at the airport, you can take a later Keisei Evening Liner train to Keisei Narita station from Keisei Ueno or Nippori station. This should give you up to one hour extra in Kyoto but it's not as convenient as changing from the Shinkansen to Narita Express at Shinagawa.

Thanks a lot everybody for all the info. Will stick to East Kyoto and will try to visit Nijo castle on December 25.
Will post a report when I get back.

Was thinking of taking the Skyliner or a Keisei limited express into Narita. They seem to be running quite late.

Skyliner does not stop at Narita - it blows right through. For Narita, take the local Keisei or JR train.

According to this timetable, Skyliners do stop at Keisei Narita before going on to the airport.

However, since the OP will be travelling in the evening there won't be any Skyliner but instead there are Evening liners - the last two of which do not go to the airport but terminate at Keisei Narita.

Checked Hyperdia and there is a Skyliner leaving Nippori at 21h26 and arriving at Keisei Narita at 22h21.