How is your flight scheduled? Which terminal of NRT will your flight use?
It may well be better to stay in a hotel closer to Tokyo Station if you can have time and a transportation option to get there in the night.
(Canft you have a Mt. Fuji tour on a later day? It sounds very hectic to fly into NRT late in a night and have a tour in the following morning (while you are still tired) to Mt. Fuji, which is a high mountain for which hikers and climbers should get ready well.)
Anyway, Tokyo Station of JR has seven Marunouchi gates. You need to check in advance which Marunouchi entrance you should reach by 8:00 am.
If your plane is scheduled to arrive later than 21:00, you may miss the last shuttle bus to Hilton Narita bus stop (departing at 22:20 from NRT Terminal 1 and at 22:30 from NRT Terminal 2) and the Keisei train (departing around 22:40) to catch the last shuttle bus from Keisei Narita Station bus stop (departing at 23:15).
http://www.ishinhotels.com/hilton-narita/jp/access/pdf/h_2014_04.pdfIn order to reach a Marunouchi entrance of Tokyo Station by 8:00, you will have to leave Hilton Narita very early at 6:15 or maybe earlier.
Logically you can
take a shuttle bus departing at 6:15 from Hilton Narita bus stop to Keisei Narita Station bus stop,
take a Keisei train departing at 6:45 for about 30 minutes to (Keisei) Funabashi Station,
make a transfer to JR
and take a JR Rapid train departing at 7:29 from Funabashi Station: Track 3 for about 20 minutes to Tokyo Station,
but you can get to a Sobu Underground track on the 5th basement only around 7:53, so it may be past 8:00 when you reach the designated Marunouchi entrance.
To get there earlier, you may have to leave Hilton Narita earlier and catch a taxi.