Best way to do Kanazawa and Shirakawago

I plan to see Tokyo around end March 2015 and then Shirakawago - Gokayama villages (using tour bus) and Kanazawa. Should I go to Kanazawa from Tokyo, using Kanazawa as a base or should I stay overnight in Takayama as well? The trip from Tokyo to Takayama takes 4 to 5 hours while the Shinkansen Tokyo to Kanazawa only takes 2.5 hours. I only have 4 days to see these places.
Also if I could save time travelling to get to Shirakawago, is the Noti Peninsula day trip a good idea instead of a stay in Takayama?

Stay over night in Takayama as well.
Day1 Tokyo-Takayama
Day2 Takayama-Shirakawa-go and Gokayama-Kanazawa
Day3 Kanazawa
Day4 Kanazawa-Tokyo

I'd do it this way:

Day 1: very early morning train Tokyo - Kanazawa. Either stay near the train station or in Korimbo/Kawaramachi. Visit the Tourist info in the JR station for really good help with any queries you have. Drop bags and go for sushi lunch in Omicho Market. After lunch go to Kenrokuen and C21st Museum.

Day 2: More time in Kanazawa. Aim to see some of the: handicrafts, gold leaf, lacquerware, samurai districts, geisha districts, etc.

Day 3: a couple of hours free time in K'zawa. Lunchtime/early afternoon bus to Shirakawa, giving you a couple of hours there before darkness (that's all you need to see the place). Stay overnight in Shirakawa (which is the real point of going there, imho).

Day 4: early bus to Takayama. Drop bags at bus station in lockers. Hida beef lunch in the old part of Takayama (5-10 mins walk), then do the festival float hall in the afternoon (walking from one to the other will give you some nice views and take you along the river). Late afternoon/early evening train back to Tokyo.

Thank you for both very prompt replies. Much appreciated as it is my first time use.

I particularly like the details provided by Winter Visitor and will check it out.