Travelling to Tokyo, Kyoto, Osaka and return

Hi there
we're visiting Japan from 28th June to 11th July. From 28th June to 2nd July we'll be in Tokyo; from 3rd July onwards we're travelling in the Kyoto, Osaka, Kobe area, returning back to Tokyo on 9th July.
My question is...should we buy a 14 day or 7 day JR pass...? I believe when we're in Tokyo we're more inclined to use the subway and that the JR pass is better if you're travelling outside of Tokyo....is that correct?
Many tks
Samantha