I had a good experience with Sakura House. Their guest houses are nice, everyone gets their own bedroom with a common kitchen/living area, and not as expensive as your own apartment. You're best off having them show you places so you can make an informed decision about the place. I got a place without looking at it, and it turned out to be too close to a train station (I had to wear earplugs to sleep). But they have a lot of places all over the city, so you can easily find something convenient to where you want to be that works for you.