You can't go all the way to Kawaguchiko on JR. You can only go as far as Otsuki. There are a few direct limited express trains there from Shinjuku, but most of the time you will need to transfer.
The Fujikyu train from Otsuki to Kawaguchiko takes about 55 minutes and costs 1140 yen.
You can't buy a Fujikyu train ticket at the JR office. You have to get it at Otsuki. The Narita Express does not go to Otsuki either. Please use Hyperdia to find the best time and train.
Actually you can use your JR Pass to take the Narita Express 8 from Shinjuku to Kawaguchiko. This N'EX train exceptionally runs on Saturdays and holidays only, leaving at 10:47 from Shinjuku and arriving at 12:43 in Kawaguchiko. See this handy JR EAST pdf for more info:
While it's a JR train, going to Kawaguchiko means that it runs partially on non-JR lines, so yes there are additional fees to pay when using the JR Pass to ride.
Comments
The Fujikyu train from Otsuki to Kawaguchiko takes about 55 minutes and costs 1140 yen.
You can see regular fares, routes and schedules on Hyperdia.
http://www.hyperdia.com
So when I make the reservation on the ticketing office, I have to pay extra 1140yen for the direct train?
You have to get it at Otsuki. The Narita Express does not go to Otsuki either. Please use Hyperdia to find the best time and train.
Actually you can use your JR Pass to take the Narita Express 8 from Shinjuku to Kawaguchiko. This N'EX train exceptionally runs on Saturdays and holidays only, leaving at 10:47 from Shinjuku and arriving at 12:43 in Kawaguchiko. See this handy JR EAST pdf for more info:
https://www.jreast.co.jp/hachioji/info/20160720/20160720_nex_info_e.pdf
While it's a JR train, going to Kawaguchiko means that it runs partially on non-JR lines, so yes there are additional fees to pay when using the JR Pass to ride.
Hope this helps.
Japan Experience
"N'EX (Narita Express) No.8/No.41 [Service Dates] Saturdays and holidays until September 25th".
They obviously both can't be correct.