Look at some of the local chains of business hotels. There's a Washington something one next to the Big Sight (convention center on the island) and another one (I forget the name) next to the Park Hyatt in Shinjuku. You should expect a small room with a small bathroom, TV mounted on the wall, vending machines, and a clientele that expects good wifi.

Another idea would be the less expensive properties in the Prince (Japanese) chain.

There are boutique hotels in Japan too. For example, there's a newish one across the major side street from the Imperial Hotel

For a longer stay, International House if you can get a reservation. The Tokyo one is in Roppongi while in Osaka it's near the old (non-science) campus of Osaka University.