The owners of this company certainly know Japan better than most, and can help with introductions to craftspeople etc. if you want a bespoke itinerary. If you're looking for an agent who will work with you to plan interesting experiences, it would be worth having a discussion with them.
https://tokyoway.jp/

If you haven't a clue about what interests you or what you want from your trip, you're better off with a more traditional Japanese agency like the JTB etc. listed above. They'll put together a plan with the highlights.