Terminal 1 rooftop deck
6F open-air observation deck on the west side. Free to enter, faces directly towards Fuji. Best 1 hour after sunrise.

Airport
Tokyo Haneda Airport sits roughly 95 km east of Mount Fuji. On clear winter mornings the entire cone is visible from the western runways and terminal observation decks.
6F open-air observation deck on the west side. Free to enter, faces directly towards Fuji. Best 1 hour after sunrise.
5F observation deck. Faces the bay, but Fuji shows clearly over the runways on bright winter days.
5F Edo Market and the 5F observation deck. Look west past the control tower around dawn for the cleanest air.
Heading to Osaka, Fukuoka, Okinawa, Korea, China or Southeast Asia: sit on the right side (K seats). Fuji appears 20-35 minutes after takeoff depending on departure runway.
From the Pacific or US west coast, ask for the right side. From within Japan, left side westbound to eastbound. Approach paths shift by wind direction so it is not guaranteed.
Keio and Fujikyu run direct highway buses from HND to Kawaguchiko in about 2h45. Around 2,500 yen. Best if you have luggage.
Keikyu line to Shinagawa, JR to Shinjuku, then JR Chuo + Fujikyuko line or the Fuji Excursion limited express. About 3 hours total. Covered by JR Pass on the JR legs.
Keikyu to Shinagawa, Tokaido Shinkansen to Odawara, then Hakone Tozan. About 2 hours and gives the iconic Fuji view from Lake Ashi.
A JR Pass covers Shinkansen and the JR legs from Haneda to the Fuji area. Buy it before you fly via getjrpass.com and pick up your pass at any major JR station.