Places outside of Tokyo to see on rainy days?

So currently my family and I are staying near Shinjuku Station. We initially planned to go to Enoshima island tomorrow but the forecast states a likely chance to rain. So does anyone have good suggestions to visit outside of Tokyo that is indoors? This is our first time in Japan.

A good quality rain jacket can save the day. Tested, worked, when i had trip with my family to Nikko (half day with constant medium (heavy by Estonian standards) rain) and Izu Shaboten zoo (also, half day had not so pleasant rain).

When it is raining or weather in general is miserable - i would recommend an onsen city which has good public baths.

Near the Tokyo i have visited Kusatsu onsen and Oedo onsen near the Takao station. I would recommend both as daytrip.

Should i have again a chance to visit Tokyo as a base city - then i would consider also a public bath little bit of north of Keio Chofu station, and also Ikaho Onsen, Nasu and Nasu Shiobara onsen, Zao onsen and maybe even Nyuto onsen, although the last one as daytrip from Tokyo seems practically non-doable due the 2 hour gap on the bus schedule between Tazawako station and Nyuto onsen before 12:00 (i.e even taking the first Akita shinkansen is too late to catch the suitable bus).
Of course, those long daytrips make IMHO only sense if you have some kind of railpass.

BR,
Lauri

Indoor activities outside Tokyo is a bit vague.
The cup noodles museum in Yokohama? Does it need to be outside Tokyo? There are plenty of museums in Tokyo (I liked the Sato Sakura museum, although it's small).

I second the suggestion about onsens from the PP, IMO having a hot bath under the rain is a fantastic experience (although I have to admit I did not try that while it's 30‹C+ outside). If you don't have a pass or don't want to travel too much, you could fallback to a sento/super sento/spa in Tokyo.

If this is for today 30/aug with the intense rain I would stay in Tokyo. There is a risk that trains may get interrupted. A few lines are already eg between Atami and Odawara.
See example here from JR:

https://traininfo.jreast.co.jp/train_info/e/kanto.aspx

There are more than enough museums , shopping (if thatfs your thing) and onsen inside the city to enjoy a rainy day.
Itfs going to be rainy tomorrow as well but lighter rain. So then you can venture outside of the city.

If youfre nearing the end of your trip and have some luggage space left, shopping is a good thing to do on a rainy day (for some people, at least). You donft have to leave Tokyo to do that, but if you want to take the better part of a day and experience the largest shopping mall in Japan (unapologetically western style, but there are a lot of good Japanese brand stores and a huge range of merchandise, including two large supermarkets, also a full-size outlet mall), you could head out to the Aeon Laketown Mall in Saitama. Itfs my own personal favorite.