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Shirakawa Go is definitely a place to visit but I probably wouldn't want to stay overnight.

I did spend the night in Hakone to experience a Ryokan. It might be a place you wish to stay for two nights.

How are you traveling? Car? Train? Bus?

If we go to Shirakawa Go, we would stay in Takayama. Most likely travel by train

Hakone is between Tokyo and Kyoto. It is very easy to “bullet” from Tokyo to Hakone, spend the night(s), then continue to Kyoto on the train. That would be my recommendation. I have done that several times with up to 3 overnights.

Nikko is the opposite direction from Tokyo if headed toward Kyoto. Train would require return through Tokyo.

Shirakawa-go is a bus or car route. “ Tamayaka” do you mean Takayama? Not as direct as Hakone between Tokyo and Kyoto for a short stay. Same issue with lake Kawaguchiko. I assume Takayama with day trip in full day to Shirakawa? Have you checked routes or tours? If you do this, get the bus tickets in advance - they can sell out.

First trip ? Hakone would be easiest - volcanic areas; lake area with temple, check point, Old Tokaido Road hiking; Open Air Museum and other art museums; various transport routes. Lots to do - I made two trips of 3 nights each in 2033 and 2024 without repeating. A couple days gives lots of options. Lots of ryokans. It’s all luck of the draw, but I had multiple days of terrific Fuji views during your timeframe - here’s hoping!

Nikko was awesome.

We stayed in a ryokan at Takayama and enjoyed it. It has a nice old town to explore But I haven’t been to the other places on your list for comparison, so can’t say if it’s the best choice of those.
We also like nature and smaller villages - of the places we went to on our trip on Honshu, Tsumago, Magome and Narai were the nicest, also surrounded by nice walking trails.

Agreed Nikko would be a great 2 day, 1 night trip - but in the wrong direction by train. I have not stayed at most of the others you listed, but recently wound up with 2 days, 1 night on Lake Ashi at a very nice hotel with onsen, Mt. Fuji views, cable car, and nice walking. It was on a Shinkansen route Kyoto to Odawara, then Odawara to Tokyo (with a one hour free hotel shuttle from the train station to the lake and hotel).

Bus company for Takayama and Shirakawa. I have used them, reliable, easy. I needed to cancel one trip - no difficulties. Everything can be done online.

https://www.nouhibus.co.jp/english/

Nikko is also a popular one day trip from Tokyo. Some try to cram in the temple area and the slightly farther out National Park via bus from near train station in one day, but I, personally, would choose one or the other. (Caveat - I am an "in depth" traveler while others prefer short stops and drive throughs at more places). There are pass "deals" from the Tobu Railway: https://www.tobu.co.jp/en/service/tourist/ . Some opt for bus tours from Tokyo - I haven't done that; traffic could be a difficulty.

If you are doing one day trip from Tokyo - Kamakura is a bit easier with more train options and less travel time. Both Nikko and Kamakura are great - you won't loose with either choice.

I'm glad you clarified Tamayaka for Takayama. I liked Takayama. The historic old town was interesting to explore.

Considering when you are going, Hakone is on a lake and it might be cold by the time you get there. If there are Ryokans that you like in Takayama, I'd suggest looking into them. That way, you could experience a Ryokan and visit Shirakawa-go.

Make sure you are leaving enough time for Kyoto and surrounding places like Nara.

Thanks everyone. Deciding between all these options is the hard part. Not trying to compare Mt Fuji to Rainier- but I live in Seattle and realize that if there is cloud cover, it might be tough to see the mountain.
Would love to see traditional villages and the alps, which I why I am torn about Takayama/Shirakawa-go.
Sounds like Nikko and Hakone are easier to get to?

With a short time frame, Hakone is likely the most efficient stop between Tokyo and Kyoto. By train: Tokyo - Odawara -Hakoneyumoto. The transfer at Odawara is very easy - the area is set up for day trippers catching the onward train to Hakoneyumoto. (From Odawara, there may be other onwards routes depending on where a person is staying. Many hotels/royukans pick up at Hakoneyumoto. ) When leaving, Hakoneyumoto - Odawara - Kyoto.

Nikko: By train: Tokyo - Nikko - Tokyo - Kyoto. There would likely be a change of train stations in Tokyo after returning from Nikko for the onward journey to Kyoto. There are several train options using different stations.

Takayama: Tokyo - Nagoya (most likely transfer station) - Takayama. No onward train to Shirakawa. You need the Nohi bus. There may be day tours from Takayama to Shirakawa that would return you to Takayama. To get to Kyoto: Takayama - transfer Nagoya or elsewhere - Kyoto

Another option is Tokyo - Nagoya - Takayama - bus to Shirakawa continuing bus onward to Kanazawa - back to train at Kanazawa to Kyoto. A lot of travel for two days, in my opinion.

You can check routes and times with a website or app like Jorudan or Navitime (I like the apps better than the websites.)
https://world.jorudan.co.jp/mln/en/?sub_lang=nosub
https://japantravel.navitime.com/en/

Wow thank you for all the information! Really appreciate all this!

Kamakura has nice Ryokans and great walking trails and small temples. it may be worth an over nite
Hakone would be your best - it has beautiful Ryokans, boat rides on the Lake, Outdoor Picasso museum. Hakone is very famous for their Onsens. Beautiful views of Mt. Fuji

Nikko is beautiful but hard to get to and lots of stairs to all of their temples.

Enjoy!

How about stopping along the Nakasendo Trail and visiting 2 post towns, Magome and Tsumago? You would take the Shinkansen to Nagoya, and then a more local train to Nakatsugawa. Either bus or taxi to Magome 30-45 min away, spend time to exploring Magome, and then hike about 7 km to Tsumago. You are in rural Japan. After exploring this more sleepy post town, spend a night at Takimi Onsen. The owner picks you up from Tsumago and his place is located in the woods 15-20 min away. The highlights are - you are the only group in this traditional home, complete with separate indoor and outdoor onsens for men and women which overlook the woods and some waterfalls. Lots of original artwork, crafts, decorations in this rustic home. Spotless clean as is everything in Japan. And best of all the kind owner is a retired chef from one of the big Tokyo hotels and cooks an amazing traditional dinner and breakfast. In the morning he will drive you to the nearby train station where you catch 2 local trains to get back to Nagoya and then the Shinkansen to Kyoto. I found the Really Rural Japan website really helpful and found the owner Michael very responsive to my email queries. We booked a day tour Magome-Tsumago with his associate Sachi - unfortunately it was pouring rain - but the mountainy rural area was still very beautiful. We were just there 2 weeks ago and did this trip from Kyoto..