They look like pretty good tours - particularly with a volunteer tour guide, which would give you a better insight to the city than a drive by on Hato Bus.

I can recommend the Mt. Fuji/Hakone day tour with Sunrise Tours. We booked it through Viator on their website. They pick up at certain hotels, otherwise you have to get to Hamamatsucho Bus station - you will also be dropped off at Shinjuku or Tokyo Station on your return. The transportation system is so easy to use that we had no problems, even with it being our first day in Tokyo. I would also suggest opting for the traditional Japanese lunch.

We took the mt fuji-hakone tour wit H.I.S. tours; it was OK and included drop off at our pick-up hotel.

I can also vouch for SUnrise Tours Mt. Fuji/Hakone tour- I did it when I lived in Japan with family and it was great, as was their day trip to Nikko.

For the tours listed on the website link you provided, you can easily do almost all of those on your own with a good guidebook, especially with a guidebook that has a walking route mapped out in it.

Some of the more upscale hotels have a tea ceremony that you can do- I did one at the New Otani- you don't need to be a hotel guest.

If you are comfortable enough I would reccommend doing it on your own and reading about the places in the book as you go along. The DK Eyewitness Japan/Tokyo guidebooks are great for things like this.