Highly recommend DOMO! They are close to 2 JR stations (Okubo and Shin-Okubo), only a 3 minute walk, best way to find them is if you google DOMO cafe on google.
It’s a very clean, cosy, easily accessible apartment (elevator), and they also offer free breakfast (vegetarian friendly too), although it’s small serving, we were very grateful we didn’t need to find breakfast + coffee.
If you are buying a JR pass, you may not need to buy a metro pass as well.
Great place to stay for 5 days!