Housecom is a Japanese realtor company that is friendly to foreigners, as far as I can tell, from a personal experience I had. I recommend trying them.
This information may be offensively obvious to the seasoned expats, but it is not obvious to newbies.
I know a lot of people who are still going through the BS of being sat at realtor companies while the realtor calls 20 landlords, ending each convo with "Ah no foreigners? Sorry to bother you!" (Did not have that experience with Housecom at all) Or worse, they're using realtor companies like Tokyo Best Realtors.
edit3: length – I had information to support what I thought but it was long, and that seemed to bother people.