For the most part you won't need any other passes for local city travel except maybe the 500yen 1-day bus pass for KyotoIn Kyoto, unless you are headed to Fushimi inari or Uji or something like that you won't be using the JR pass much.
Kanazawa you will definately not be using the JR pass for local city travel.
Probably only Tokyo.
As the above commenter said, use http://www.hyperdia.com to figure out what trains you need to take and calculate your costs on JR trains to see if it's worth it
Or you can consider taking a highway bus instead to save money.