My current plans are to get a place in the Shinjuku area, and my departing flight from Tokyo is at 9:30 AM on a weekday. I would need to get to the airport around 6:30 AM, and probably leave the hotel around 5 AM to catch the JR to NRT. Do you recommend I stay in a different area to make my commute to NRT more convenient considering the time of my morning flight? Will the JR be crowded with morning rush hour?

I was planning on having a Tokyo wide pass during the end of my trip to cover the cost of the JR train to the airport.