travel to Kanazawa and Takayama

I plan to visit in October, arriving in Tokyo. I want to visit Kyoto, Kanazawa and Takayama (want to see Hida village). Should I stay one night in Takayama or simply take a day trip from Kanazawa? Should I go to Kanazawa first, then Takayama? Is it easier to travel from Tokyo or Kyoto?

Should I stay one night in Takayama or simply take a day trip from Kanazawa?

It takes more than 6 hours of traveling to go from Kanazawa to Takayama and back. Therefore, I recommend to stay at least one night in Takayama.

But Shirakawago, just one hour from Kanazawa, can be visited in a day trip:
http://www.japan-guide.com/e/e5950.html

Is it easier to travel from Tokyo or Kyoto?

From Kyoto. By about one hour:
http://www.japan-guide.com/e/e5908.html

Firstly, You might contemplate purchasing a seven-day Japan Rail Pass if you're flying into and out of Narita. It's 28,300 yen and valid for consecutive 7 days.

I would suggest you to make a route in the order of Tokyo--transfer at Nagoya--Takayama--transfer at Toyama--Kanazawa--Kyoto--Tokyo. This seems to be more efficient routing considering your desired cities's locations. You might want to stay in Takayama overnight.

If you fly into Tokyo and out of Osaka Kansai, using buses works out much cheaper than trains.
Narita--Tokyo: JR Narita Express train, around 3,000yen, Limousine bus, 3,000yen or Keisei Skyliner train, 1,920yen
Tokyo (Shinjuku)--Takayama bus: 5.5hours, 6,500yen and departures; 6:30, 8:00, 13:30 and 15:30
Takayama--Kanazawa bus: 3hours, 3,300yen and departures: 9:30 and 15:20
Kanazawa--Kyoto bus: 4hours 20minutes, 4,060yen and departures; 7:00, 8:30, 10:00 and 15:30, though on this segment, the train runs every 30 minutes, takes 2hour 10minutes and costs 6,910yen.
Kyoto--Osaka Kansai AIrport bus: 1hour 45minutes, 2,300yen, very frequent departure

Thank you, uji and optimistk, for your helpful suggestions. I am flying in and out of Narita and will spend 14 nights in Japan. Due to a desire to visit Kobo-san flea market on 10/21, I will need to go from Tokyo to Kyoto first, then travel to Kanazawa/Takayama and then back to Tokyo. Would you suggest going to Takayama first or to Kanazawa first (what is easier/quicker for train travel purposes)? Also, is it
worthwhile for me to purchase a 14-day Japan RailPass and, if so, is it worthwhile to pay for the green car rail pass? Thank you again for any help

A 14 day rail pass will cost about the same as regular tickets. So, I think it is worth it.

is it worthwhile to pay for the green car rail pass?

Only if you are a person who likes paying a little bit more for a little bit luxury.