Have you heard of Hakone before? It’s a pretty popular destination for tourists and residence alike! It is convenient to get to from Tokyo so you can go for a daytrip, but I recommend spending at least one night there.
Hakone is a little mountain town and a natural hot springs area with a lake, and much more. There are many traditional Japanese inns (ryokan) but you can find modern hotels like Hyatt there too. The ryokans are nice because they have onsens, many with private baths in your room or that you can reserve for private use. Usually your breakfast and dinner are included in the room reservation at ryokans, which is nice since you are usually going there to relax and enjoy the experience.
I think autumn is the best time to go because of the nice weather and the beautiful fall colors. It’s also great to enjoy the hot springs when the heat of summer is gone. Of course, any season is nice though!
Another place to go is the Open Air Museum. It is an art museum with most exhibits outdoors in a beautiful park.