All the subway lines are non-JR lines,
which are not covered by any JR pass.
[Saving your time]
JR Tokyo Wide Pass is good for 3 consecutive days.
It sounds a tight schedule
to do these three round trips from Tsukiji within only 3 days.
Staying overnight
near Nikko or Tobu-nikko Station / Karuizawa Station,
you can save your traveling time
by making a transfer between the Shinkansen
at Omiya (#) Station for Karuizawa / Utsunomiya.
(#) Here "O" is pronounced long.
[Ueno transfer]
Tsukiji > Karuizawa = Hibiya Line to Ginza / Shinkansen Hakutaka to Karuizawa This Ginza should be Ueno, to be precise.
From subway Ueno Station's Hibiya Line gates,
even the nearest JR gate is a little apart.
I recommend
you expect for the transfer at least 15 minutes
(from the subway arrival until the Shinkansen departure).
https://www.tokyometro.jp/station/ueno/yardmap/index.htmlYou go on the pathway to the Ginza Line concourse,
turn to the right,
walk more
until you see on your left the escalator up for JR,
go up the escalator, and turn to the right;
you find the Central Gate of (JR) Ueno Station.
To use the Shinkansen,
you pass through also the Shinkansen transfer gate.
The Shinkansen platforms of Ueno Station
are on the 4th basement.
[JR-Tobu through Limited Express]
This pass is valid
for rides of JR-Tobu through Limited Express trains,
which connect the JR stations
(Shinjuku, Ikebukuro, Urawa and Omiya)
and the Tobu stations on the Nikko and Kinugawa Lines.
To get to Nikko in the morning,
you can take the through Limited Express Nikko 1,
as long as you can reserve your seat.
Tsukiji Station ( H-10 )
{ Dpt. around 6:40 }
( Track 1 )
| Tokyo Metro Hibiya Line
| : Train for Naka-meguro
( Track 5 )
( H-08 ) Ginza ( M-16 )
https://www.tokyometro.jp/station/yardmap_img/_station_%E9%8A%80%E5%BA...{ Dpt. around 6:50 }
( Track 4 )
| Tokyo Metro Marunouchi Line
| : Train for Ikebukuro
{ Arr. around 7:10 }
( M-25 ) Ikebukuro
: Short transfer via the pathway outside the gates.
Ikebukuro
{ Dpt. 7:36 }
( Track 3 )
| JR + Tobu: Limited Express Nikko 1
{ Arr. 9:28 }
Tobu-nikko.