Individual Day Tours in Japan?

We always had good luck using the Things to do pull-down menu on TripAdvisor while researching day trips and tour providers everywhere in Japan.
Conducting individual searches for the cities you've mentioned should turn up a number of potential excursions that might be of interest and, FWIW, we always found the posted reviews to be pretty reliable in helping to sort thru the various options.

Here is a 2-day guided tour of Tokyo with a reputable walking company. They run from 8:30 or 9 to 5 on each of the 2 successive days; they do not include lodging or meals. Maximum group size 12; focus is on history.
https://walkjapan.com/tour/tokyo-tour?

Check the Klook tours. They are like Viatour but we used them for a day trip to the DMZ in Korea and it worked easily.

Are you looking for whole day tours? I can't help there, but if you just want something to fill a few hours of a day check out:

• Tokyo Localized (https://www.tokyolocalized.com/) - "free" walking tours of the most popular Tokyo districts (you'll need to tip)
• Kyoto Localized (https://www.kyotolocalized.com/) - same deal except Kyoto

For food tours specifically I recommend Ninja Food Tours (https://www.ninjafoodtours.com/). I did 2 in Tokyo. They have a Kyoto offering too, but at the time availability was limited so I didn't get to try it.

Also, check out AirBNB Experiences. Lots of great tours, both walking and food, and other experiences.

Thanks for the input all!

Food tours are def of interest so appreciate the recommendations on that front!

I'm not necessarily looking for all day tours (though if anyone has a great driver/tour guide for Kyoto I am considering doing that for a day) but in general just looking for short term tours/ 2-4 hours/ to give context to an area or site.

We are actually doing a multi day WalkJapan tour for a middle leg of our itinerary when we're outside of the cities, but within the major cities we're looking for more short term stuff.

I can definitely search on Viator or trip advisor but it is really great to get a first hand account from fellow Rick Steves minded travelers:)

Kyoto is special, plan on three days there. Also, take an afternoon to visit nearby Nara.
From Tokyo, do a day trip to Nikko which is north of Tokyo. Also, see Kamakura, the giant Buddha south of Tokyo.
We did a great three day tour of Kyoto and Nara from Tokyo taking the high speed train.
Osaka is another place for a day or two, also Kobe.

I don't remember the tour company name, but check TripAdvisor.com

OK, for short tours in Kyoto we have twice toured the grounds of the Imperial Palace on the free “official” tour:

https://sankan.kunaicho.go.jp/multilingual/lang/en/information.html

https://kyoto-gosho.kunaicho.go.jp/en/visit

There is no charge and no advance signup; just go and get in the line and they will give you a lanyard with a badge and number. Last time we were there, we ended up downloading the audio guide and just using that instead of staying with the guided group.

Note that you do not go inside the buildings; you view them from the outside and learn about their history.

Consider the Culinary Backstreets food tours in Tokyo - they have two itineraries there. Their tours are excellent and include a lot of local information in addition to all the food tastings.

Fireworks festival?

https://web-Japan.org/kidsweb/explore/calendar/august/hanabi.html#:~:text=From%20late%20July%20to%20late,summers%20seem%20fun%20and%20exciting.

In Kyoto, I did a walking tour of the Gion area with a focus on the Geisha tradition which in Kyoto i called Gaiko or Maiko (not sure of spelling). It was very interesing. The guides also were very helpful in recommending nearby restaurants. I don't have a record of who the guide or company was -- I see there are a number of similar sounding tours advertised online.

You can do Arashiyama area or Zen Temple tour. You can check out https://gowithguide.com/ They have plenty of short day tour options.