Car

Your best option is driving, with parking lots available at all 4 of the trailheads. However, take note that on weekends and holidays, especially during autumn, the roads will be very busy and driving will be very slow. The roads around Nikko are stunning, so it might be worth taking a day off to avoid the weekend crowds if you prefer to drive.

Train & Bus

Due to the various connections required from Tokyo, if you're relying on the bus then the easiest option is to stay the night in Nikko or at the Sugamuna Campground.

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The town of Nikko is a good base for entering the national park, there is an efficient bus system that runs into the park from the town, and a direct train from Tokyo that takes two hours. The bus from Nikko town to Lake Chuzenji takes about 45 mins to 1 hour depending on traffic. All the bus times are available on Google Maps, here's an overview:

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Yumoto Onsen Trail

Lake Chuzenji ​→ Bus → Yumoto Onsen Trail = 40 mins

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Sugamuma Trail

Yumoto Onsen ​→ Bus → Sugamuma Campground = 15 mins

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Nikko-Shirane Ropeway Trail

Yumoto Onsen ​→ Bus → Ropeway = 40 mins

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Bus Pass: For public transport, I recommend getting the Nikko all-area pass (4,780 yen), available from the TOBU Info Center in Asakusa, it includes a 20% discount on limited express train tickets and unlimited bus rides inside the park. If taking the cheaper the local trains or driving, you can just buy a bus pass from the Tourist Info Centre at Nikko station (2,650 yen) which gives you unlimited rides into the national park.

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Tokyo: Nikko station is 2 hours from Asakusa in Tokyo and the train costs about ¥3000. Or you can catch the local trains with 1 or 2 connections and save about ¥1000 for an extra half hour of travel time. You can also catch local trains from Shinjuku for about ¥2000.

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Crowds: During autumn (Sep/Oct) and on long weekends, crowds in Nikko can be pretty intense. The traffic can also become very congested, sometimes doubling the travel time by both car and bus.