Kamen Rider goods can be found most places where you can find anime. For the current series, you'll probably do well searching in mainstream toy stores. In Tokyo, this includes Toys R Us (which has stores in Odaiba and the Sunshine City complex in Ikebukuro) or Kiddyland.
For older series, check out the used toy shops you find around town. In the Tokyo area, this might include the Mandarake stores in Akihabara and Shibuya. Nakano Broadway may be another fruitful place to look. The Book Off chain is likely to have photobooks and soundtracks from older series as well.
There's no museum in the Tokyo area at this time, but you might want to check out Kamen Rider The Diner. It's a restaurant in Ikebukuro that looks like a Shocker secret base, with food and drink selections themed after various Kamen Rider shows.
If you're visiting Kyoto, check out Toei Kyoto Studio Park to see Hero Land, where Kamen Rider and Super Sentai artifacts are displayed. There was a Hero Museum in Chiba as well, but it closed in early 2017.