In a summary, you could do Dragondola and Yahiko Park in a day.
Tokyo 608-724 Echigo-Yuzawa 820-857 Naeba Prince Hotel 1240-1322 Echigo-Yuzawa 1401-1555 Yahiko 1821-2100 Tokyo
But, I might pefer Yahiko as one, Okutadami and Nagaoka Momijien as one, or Echigo-Yuzawa as one.
Tokyo 748-1032 Yahiko 1721-1952 Tokyo
Tokyo 608-737 Urasa 750-905 Okutadami Dam (30 min Okutadami Round course boat) 1135-1235 Urasa 1248-1405 Nagaoka Momijen 1605-1840 Tokyo
Tokyo 608-724 Echigo-Yuzawa 755-822 Daigenta Canyon 1034-1100 Echigo-Yuzawa 1140-1217 Naeba Prince Hotel 1400-1442 Echigo-Yuzawa 1510-1533 Kiyotsukyo 1747-1813 Echigo-Yuzawa 1828-1952 Tokyo
The followings are the materials with which I have reached the conclusion above.
Jorudan lists nine sites for Niigata prefecture in late October.
https://sp.jorudan.co.jp/leaf/migoro_10c_4.html
Yahiko Koen Momijidani (1st in Koyo popularity in Niigata: late Oct - mid-Nov) https://sp.jorudan.co.jp/leaf/spot_55024.html
Just in front of JR Yahiko station
Okutadamiko (2nd in Niigata: mid-Oct - late Oct) https://sp.jorudan.co.jp/leaf/spot_55023.html
1h20m bus ride from JR Urasa and 10 min walk from the bus stop
Myoko Kogen Imori Ike (3rd in Niigata: mid-Oct - early Nov) https://sp.jorudan.co.jp/leaf/spot_55022.html
15 min bus from Myoko Kogen station.
Momijien (4th in Niigata: late Oct - mid-Nov) https://sp.jorudan.co.jp/leaf/spot_55020.html
10 min walk from JR Raikoji in Nagaoka city
Kiyotsukyo (5th in Niigata: mid-Oct - early Nov) https://sp.jorudan.co.jp/leaf/spot_55021.html
23 min bus from JR Echigo-Yuzawa and 25 min walk from the bus stop
Arakawa Kyoukoku Momiji Line (6th in Niigata: late Oct - early Nov) https://sp.jorudan.co.jp/leaf/spot_55026.html
It needs a car to get there.
Aganogawa Rhein Funakudari (7th in Niigata: late Oct - mid-Nov) https://sp.jorudan.co.jp/leaf/spot_55025.html
It needs a car to get there.
Dragondora Tashiro Ropeway Naeba Ski Resort (mid-Oct - mid-Nov) https://sp.jorudan.co.jp/leaf/spot_J0169.html
50 min bus from JR Echigo-Yuzawa, 25 min Koyo viewing from the ropeway
Daigenta Canyon (mid-Oct - early Nov) https://sp.jorudan.co.jp/leaf/spot_J0170.html
20 min from JR Echigo-Yuzawa, there would be rental rowling boats.
1. Yahiko Park is near JR Yahiko, but Yahiko Shrine, 15 min walk needed, should be regarded as a must. Jalan rates Yahiko Shrine as #1 destination (not limited to Koyo) in Niigata Prefecture in October. There is Otorii along the railway toward Yahiko. You may consider Yahikosan Ropeway as well. Yahikosan Skyline road also has an entry in Jalan. Jalan estimates 2 hours each for Yahiko Park, Yahiko Shrine, and Yahiko Ropeway, and 3 hours for Mt Yahiko. You could arrive there at around 11:00 from Tokyo. You would have 6 hours before it gets dark. If you just do Yahiko Park, you could leave here early afternoon.
https://www.jalan.net/kankou/spt_15342ah3332082764/http://www.yahiko-jinjya.or.jp/http://www.yahiko-jinjya.or.jp/meguru/index.htmlhttps://www.jalan.net/kankou/spt_15342ag2130009863/https://www.jalan.net/kankou/spt_15342ae2182089519/https://www.hotel-juraku.co.jp/yahiko/https://www.jalan.net/kankou/spt_15342ee4572082681/https://www.jalan.net/kankou/spt_15342ab2012089510/https://www.jalan.net/kankou/spt_15342aj2202082487/2. Here is the Timetable for Okutadami.
http://www.minamiechigo.co.jp/pdf/jikoku-300401/koide/okutadami.pdfOkutadami is the gateway to Oze in summer. That route will be shut down on 15 Oct. The boat to Ozeguchi and the following bus to Numayama Pass are to be closed on that day. The route over Shiori Pass to Ginzandaira will be closed on the previous day.
http://okutadami.co.jp/boat/route_ozeguchi.htmlThe remaining parts are operating until the Koyo season would be over.
Okutadami Round course boat until 8 Nov.
http://okutadami.co.jp/boat/route_okutadami.htmlGinzandaira course boat until 6 Nov.
http://okutadami.co.jp/boat/route_ginzan.htmlThe bus to Okutadami Dam until 3 Nov. This bus goes through Okutadami Silver Line road. Jalan estimates one hour for it.
https://www.jalan.net/kankou/spt_guide000000172309/Tokyo 608-737 Urasa 750-905 Okutadami Dam (30 min Okutadami Round course boat) 1135-1235 Urasa 1355-1528 Tokyo
3. Myoko Kogen is at the Hokuriku Shinkansen side. Jalan estimates one hour for Imori Ike and 2 hours for Sky Cable.
https://www.jalan.net/kankou/spt_guide000000176644/https://www.jalan.net/kankou/spt_15217ee4572089869/4. Jalan estimates 2 hours for Nagaoka Momijien.
https://www.jalan.net/kankou/spt_guide000000176645/5. Echigo-Yuzawa has three Koyo sites.
Jalan estimates 2 hours for Kiyotsukyo. Here is the timetable for Kiyotsukyo.
http://www.minamiechigo.co.jp/pdf/jikoku-300401/muikamachi/morimiyanoh...https://www.jalan.net/kankou/spt_15210ab2042089120/Jalan has an entry for Naeba, stating half a day. But it is for a ski resort in winter. It would be 2 hours by an estimate for Myoko Kogen Sky Cable above. Here is the timetable for Naeba.
http://www.minamiechigo.co.jp/pdf/jikoku-300401/muikamachi/crystal.pdfhttps://www.jalan.net/kankou/spt_15461ca3470058299/No entry for Daigenta Canyon by Jalan. I assume 2 hours. Here is the timetable for Daigenta Canyon.
https://sp.jorudan.co.jp/leaf/spot_J0170.html
You may marginally do all the three in a day from Tokyo, though this one includes one hour dark time at Kiyotsukyo.
Tokyo 608-724 Echigo-Yuzawa 755-822 Daigenta Canyon 1034-1100 Echigo-Yuzawa 1140-1217 Naeba Prince Hotel 1400-1442 Echigo-Yuzawa 1510-1533 Kiyotsukyo 1747-1813 Echigo-Yuzawa 1828-1952 Tokyo