In Tokyo you can make very good use of the JR Pass by using JR lines to get to many of the sights. Here's a map of JR lines in Tokyo for reference. In general however you will need to purchase some metro travel to get to certain locations. Osaka has some JR coverage, but you'll find you need to use more of the metro here. Kyoto is mainly serviced by non-JR bus and metro services which will not be covered by the JR Pass.
Your options for using these municipal networks are:
- Individual tickets as needed
- Prepaid travel credit card
- 1 or 2 day free passes
Prepaid cards don't offer cost savings over individual tickets, but do make using travel easier as you don't have to think so much about purchasing tickets at each stop.
Whether a local metro pass makes sense for you vs just purchasing tickets or a prepaid travel card very much depends on the amounts of local travel you think you'll take. For metro travel you can estimate around ¥160-¥300 per trip in Tokyo. This will be roughly the range you can expect in Osaka and Kyoto too.
You can find out more on the passes for each of these cities at the following pages:
- Tokyo Metro Passes
- Osaka Metro Passes
- Kyoto Metro/Bus passes
Hope this helps!