How is your whole itinerary?
Would you just visit Hakone and leave Japan?@
VMC:
Also JR-East LtdExp #Super View Odoriko and (regular) #Odoriko are online booking possible at JR-East web. Unfortunately that reservation system does not work for your case,
as long as you plan to leave Tokyo for Hakone on Day 1,
because it requires you to pick up your tickets by the night (at 21:00 Japan Standard Time) before the boarding date.
You can try to reserve your seats in JR Shinkansen and Limited Express trains (e.g. Narita Express trains)
at JR East Travel Center in NRT Terminal 1 | 2 or,
while the center is closed, at nearby JR Ticket Office, which is open until 21:45.
https://www.jreast.co.jp/e/customer_support/service_center.htmlCurrently there is no railway station in NRT Terminal 3.
If your flight to Narita uses Terminal 3 and you hope to reach Tokyo by railway, you go first to Terminal 2.
When Japan Rail Pass is not likely to save greatly your cost,
it is also recommendable for you to travel by Odakyu from Shinjuku on a Romancecar train.
(Some Romancecar trains run through Odakyu and Hakone Tozan Railway lines between Shinjuku and Hakone-Yumoto.)
All seats in a Romancer train require reservation.
Hakone Freepass may or may not be a god deal, depending on what sites in Hakone you visit.
Except during very late and very early hours,
there are various ways to go from Narita Airport to Tokyo's urban area:
you can go by low-cost bus (the Access Narita) to Tokyo Station
(Expressway bus terminal in front of Yaesu South Entrance, near Shinkansen gates),
by airport limousine bus to Busta Shinjuku,
by railway on a JR Narita Express train to Shinagawa Station,
where you can make a transfer to Tokaido Shinkansen,
or by railway on a JR non-Express train to Shimbashi Station,
where you can catch a train for Odawara on the (non-Shinkansen) Tokaido Line.
