There are direct limited express trains from Shinjuku to Nikko, operated jointly by Tobu and Japan Railways. See the red line on this map (the one you want to take is the red line that reaches Tobu Nikko): http://www.japan-guide.com/e/e3805.html This would be the easiest, though it comes out more expensive compared to Tobu Railways limited express from Asakusa (the blue line on the same map) or full JR trains (you take Shinkansen to Utsunomiya, then change to JR Nikko LIne to get to JR Nikko - this one would be fully covered by JR Pass if you have one). From there, you take a Tobu bus to Lake Chuzenji. You can do it in a day trip (if you just want to visit Lake Chuzenji, Kegon Waterfalls, and some of the main temples/shrines including Toshogu in central Nikko), but if you like hot springs, you can stay a night there.
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