Hi Kelli,
The JR Pass will cover travel between cities as well as the N'EX (narita express) into Tokyo. It won't cover travel on the metro. As an alternative to the metro, you can travel around tokyo using the JR Yamanote line using the JR Pass, but it's not quite as convenient.
If you're going for a 7 day trip, then using a 7 day JR Pass for the Tokyo<>Kyoto trip and the Narita express will give you a saving of ¥4820 over separate tickets:
- Narita airport terminal 1 > Tokyo: ¥3140, (62mins, 79km)
- Tokyo > Kyoto: ¥13420, (165mins, 513km)
- Kyoto > Tokyo: ¥13420, (161mins, 513km)
- Tokyo > Narita airport terminal 1: ¥3140, (58mins, 79km)
TOTAL: ¥33,120 for 4 legs vs ¥28,300 for a 7 day JR Pass
In this case, you can purchase a separate metro card for travel around Tokyo and any further trips you make on JR will add to these savings.
Hope this helps!