Besides Hakuba, Niseko and maybe one or two other places, agents sites are in Japanese and there is no unified website like realestate.com.au that Im aware of. You will need to search in Japanese and for each specific area.
My advice is if you dont plan to live in Japan dont buy here and use the money to travel to different places each year. Owning a place will definitely tie you to one location when there are so many places to go see and shred in Japan.
If you do buy a place here and plan to rent it out whilst you arent here property managers wont be interested unless they can market from Mid Dec to Early March so there goes being here in prime time. Managing it yourself from a distance is difficult (we just set up a business to help Absent Owners

) and unless you set up a business you will be stuck on tourism visas if you plan to be here an extended time. No visa also means you cant buy a car, get utilities, bank accounts etc although you can buy property insurance.
From finding the property perspective, once you find one understand older properties here are generally poorly inuslated, often near the end of their build lives and require a lot of $ to get right. Getting Japanese tradies is also a whole other issues that some of us do well with whilst others dont and you defintely want to be here to manage their work or appoint someone to supervise which we are doing now too.
Apologies for raining on your parade but having seen many with the same dream and flounder its further mentioning the above.