I went on a weekday and reached around mid afternoon. There isn't a huge crowd during that time.

It's called Hakone navi the good website.

Not far, about 10-15 min walk and the scenery will s beautiful.

If you go to Hakone shrine , to take a train and a bus . The starting location is the Hakone Yumoto Station of Odakyu line .From Hakone Yumoto Station , about 40 minutes by bus. We arrived at Motohakone Station .Look at the Lake Ashi to the left , and walk about 10 minutes , you will arrive in Hakone shrine . You if , if you want to go to the main shrine of Kuzuryu shrine , can only go by ferry , there is no way .Because , Hongu of Kuzuryu shrine is located on the banks of the lake , because you can not be reached directly .

hey :) if you going from Tokyo By Odakyu Railway Tokyo's Shinjuku Station and Hakone-Yumoto Station 85 minutes and costs 2080 yen. By slower express trains (kyuko), the journey takes about two hours, requires one transfer at Odawara Station, but costs only 1190 yen. By JR (Japan Railways) With JR trains you can only get as far as Odawara, from where you will have to use non-JR trains or buses into the Hakone area. By JR Tokaido Shinkansen you can access Odawara in about half an hour from Tokyo or Shinagawa Station (about 3500 yen one way, fully covered by the Japan Rail Pass, but not covered by the JR East Pass and JR Kanto Area Pass), but note that only Kodama trains and selected Hikari trains stop at Odawara Station. Alternatively, you can access Odawara from Tokyo in about 70-90 minutes by local or rapid trains on the JR Tokaido Main Line (stopping at Tokyo, Shimbashi and Shinagawa Stations) or the JR Shonan Shinjuku Line (stopping at Ikebukuro, Shinjuku and Shibuya Stations) for about 1500 yen one way. These are covered by the Japan Rail Pass, JR East Pass and JR Kanto Area Pass.

Buy a Hakone Freepass and take the Hakone Romancecar from Shinjuku to Gora. From there take the cable car and ropeway over the mountain to Tokendai-Ko. Jump on the Scenic Cruise and get off at Motohakone-Ko. Walk around the bay to the shrine. Alternatively, you can get any of the trains (including the Shinkansen) to Odawara and then catch a Hakone Tozan bus straight through to Motohakone-ko. But be aware that the bus is crowded and takes as long as the scenic route.