First time in Japan

Hello
We are going to japan for 11 days from 22 April till 2 May ( I know its not the best time for Japan, but we dont have another option, unfortunately)
22.04 we are arriving at Narita Tokyo and I think we will go go Kyoto and we will come back to Tokyo at 28.04 ( because of Golden week). I want to stay one or two nights in traditional guesthouse on the way from Tokyo to Kyoto. Do you recommend me where to stay? Also, what do you think about my decision to go to Kyoto before Golden week and spend time in Tokyo during this period?
Thanks a lot
Eva

I want to stay one or two nights in traditional guesthouse on the way from Tokyo to Kyoto.

What do you mean with "guesthouse"? A Ryokan? Minshuku?

Also, what do you think about my decision to go to Kyoto before Golden week and spend time in Tokyo during this period?

It depends on what you want to see in Tokyo. If you want to see Disney Resort or other destinations popular among families in Tokyo, then I recommend to do it the other way around.

Note that April 29 to May 1 is simply going to be a 3-day weekend. It will be crowded, but not in an extremely extreme way. And May 2 is going to be a regular work and school day for the majority of people. This year's Golden Week is not very favorable to the working people.

Yes, I mean ryokan or Minshuku. Two options are good for me. I don't know what town or village to choose ;( I got recommendations to Kamakura but it's very long distance for 10 days trip , I think
In Tokyo I ' m planning to visit some tourist's 'must have' , but not th dysney
Thank you

Never stayed in a ryokan as it just doesn't interest me, but Kamakura is only an hour or so from Tokyo on the Shonan Shinjuku line - not long distance at all.

Kamakura is in between Tokyo and Kyoto, so it is not a detour. However, I am not sure about the quality of the ryokans there compared to other parts in Japan. Plus you will already be visiting temples in Kyoto.

If you are looking for a top quality ryokan, then you can try some of the hot spring towns along the way. Hakone and Atami are ones that immediately come to mind. Check out the onsen listings as there are usually a high concentration of good ryokan in the area:
http://www.japan-guide.com/e/e2292.html

You could also try ryokans in western Kyoto. There are a few good rated ones in tripadvisor to the west of Arashiyama.

Kamakura is in between Tokyo and Kyoto, so it is not a detour.

It is very much a detour. Have you look at the time and number of transfer it takes to do Tokyo-Kamakura-Kyoto compared to just Tokyo-Kyoto?

Oh, missed the part where they were going en route to Kyoto. Ignore me.

@Firas
Tokyo-Kamakura - 1 hour (0 transfers)
Kamakura-Kyoto - 3 hours and 19 mins (2 transfers) using Hikari shinkansen
Tokyo-Kyoto - 2 hours 15 mins using Nozomi train

Yes, Kamakura does add a couple of hours and transfers to the trip, but that is minor if OP stays a couple of nights there if he picks this as an option. It is not drastically out of the way compared to Nikko or Takayama.

I still think Hakone and Atami are between options to find a good ryokan compared to Kamakura, but just pointing out Kamakura itself is not that bad an option.

You can look up ryokans by city here...

http://www.hostelworld.com

Kyoto has some very nice ryokan. If you have a large budget, I recommend the Tawaraya.

Otherwise, Hakone sounds like the easiest option, although I observe that ryokan there are overpriced compared to similar ryokan in less popular areas. The Izu Peninsula is another good option:
http://www.japan-guide.com/e/e6310.html

Or if you do not mind to make an off-the-beaten-path detour, I recommend Okuhida:
http://www.japan-guide.com/e/e5940.html

Thank you very much for so useful information. Now it's more clearly .
We don't want to take a car , so, we are planning to use train/buses. Is it possible and easy to getting around on public transport in area of Atami, Hakone ?

s it possible and easy to getting around on public transport in area of Atami, Hakone ?

Yes for both:
Hakone - http://www.japan-guide.com/e/e2358_008.html
Atami - http://www.japan-guide.com/e/e6317.html