Nikko, it’s a bit messy.

(i) On 16 August we will be in Shinjuko and plan to go to Nikko (note our JR Pass will not be active on this day)
(ii) On 17 August we will stay in Nikko and Okunikko (which suggests buying one of those Nikko Passes to travel around on bus may be a good idea)
(iii) On 18 we depart from Nikko and go to Shin-Osaka (this wil be the first day of our JR Pass)

Re. (iii) I assume that the journey is covered by JR Pass (JR Nikko Line to Utsunomiya+ Yamabiko to Tokyo+Hikari to Osaka). correct?
I am confused re (i) and (ii) tough. I have read that Shinjuko-Nikko is more expensive so was thinking of buying a 2 day Nikko Pass and go from Asakusa although not very convenient for us. Is this the best option, also considering that on 17 we want to visit Kanmangafuchi and Lake Chuzenji? or should we go from Shinjuko and buy a different pass? many thanks in advance for your help

Shinjuku.

@.
Boss

(iii) Yes, you are right.

(i) If you take the local JR train from Shinjuku to Omiya, let's say, and change to JR Shinkansen to Utsunomiya, then to JR Nikko line to Nikko, that (without the JR Pass) would cost 4,430 yen one way, taking about 2 hours and 10 minutes (I just did a search starting off from Shinjuku at 8:00).
If you go via Asakusa, you would need to add the time from Shinjuku to Asakusa, then change to Tobu line and everything. It's a matter of which you prefer. But you won't need the "return" leg of the pass, as you'll have activated the JR Pass on the day when you leave Nikko.
If you get to Nikko (JR Nikko and Tobu Nikko are within short walking distance) 10:30 or something in that range, you should be able to take the bus up to Lake Chuzenji, visit the Kegon waterfalls, then take the bus down to Kanmangafuchi and visit a few temples before you stay over.. in Nikko, or you might do the reverse if you are staying over in Okunikko.

(ii) One of the bus passes will pay off. Since you say Okunikko, you might have to buy the more expensive one, but a simply return trip on buses will pay off.