When it comes to hot springs there is a huge range of options, form the fanciest and most luxurious ones, to the simplest and most affordable. We visited two very different ones, the first at the hotel we stayed in Unzen (Kyushu is very famous for hot springs, together with Kumamoot and Beppu) and the other one in Hakone, near Mount Fuji (picture above), called Yuryo. It was amazing and I would recommend the day trip from Tokyo. This is the instruction flyer that we got there before entering the spa, which gives you a very good idea on the experience. The pricing can vary a lot depending on the place, but you will be surprised to see how much more affordable are spas all over the world compared to the US, Japan included! Another very famous area for onsens is near Nikko, and Kusatsu, near Nagano.
If you are only in Tokyo for few days, you can instead visit the Oedo-onsen Monogatari in Odaiba, Japan's largest hots spring resort.