Hi lovely! How exciting for you! We used the JR pass to travel within cities. It is worth the outlay especially if you are doing a lot of travelling between cities like Tokyo, Kyoto, Osaka, Hiroshima etc. as it will save you a lot of money in the long run when you add up trips.
As for travel within Tokyo, we bought a Suica card and topped it up as needed. I would recommend it and I think this is the way most locals travel too :)
Hope this helps? Let me know if you have any other questions and I will do my best to help. Otherwise have a lovely trip xx