Well you could do a day trip from Tokyo to Osaka/Kyoto but it would be lots of wasted time on the trains about 3 hours each way on the bullet train alone, not to mention local/subway trains. It wound also be exhausting so I’d stay in Tokyo for a few days and then stay in either Kyoto or Osaka for a few days, then back to Tokyo for the last day and night (if you are flying home from Haneda)
JR pass won’t pay off for a single round trip to Osaka or Kyoto from Tokyo. If you really plan to do a couple of day trips from a base in Tokyo (Tokyo to Osaka and back AND Tokyo to Kyoto and back) it will.
For me personally I would just explore Tokyo and skip Osaka/Kyoto if I only had 7 days total in Japan, there’s more than enough to keep you entertained for 1 week. 7 days is not a very long time to explore 3 cities in my view.
That being said its your trip and I get you want to see and do as much as possible so it’s totally doable, I just wouldn’t want to waste so much time on the trains if I only had 7 days. If you did one day trip from Tokyo to Osaka and back, then one day trip from Tokyo to Kyoto and back you would waste a minimum of 12 hours on the trains, that’s a full day sitting on a train, 1/7th of your trip!