If it’s your first time in Japan, I would suggest arriving at Narita at 5pm and going straight to Hakone might be slightly ambitious. Not saying it’s impossible, but negotiating the complexities of the Japanese transport system after a long flight to Narita is not something I’d recommend!
However, if you want to use the JR pass, you would take the Narita Express to Shinagawa and then catch the Shinkansen to Odawara. At Odawara Station, you can purchase Hakone Free Passes for 4,000yen per person. From Odawarra, you would take the Odakyu Line to Hakone Yumoto station. Hakone is quite spread out, but there are buses running that connect all the hotels - or you can splash out a few thousand yen on a taxi. To get out, you take the reverse route back to Odawara Station the next day.
Assuming you’re well organized and catch the Narita Express at about 5:45pm, you would probably get to your hotel by about 9:30pm. Otherwise, after 10:30pm is likely.
I also looked for some buses that go direct from Narita Airport to Hakone, but couldn’t find any. Accessing Hakone from central Tokyo tends to be easier.