Mimaru Ikebukuro was an excellent fit for our family trip (me, husband, toddler, and mother-in-law). It was the only place I found in central Tokyo with a 2-bedroom apartment-style hotel room. The size & layout of the apartment was thoughtful, and the amenities were great (e.g. highchair & crib provided, towels changed daily, washer/dryer in unit, etc.).
Staying in the Ikebukuro neighborhood was great; there are lots of good restaurants and shops around, and the local train station is a major transit hub - perfect for sightseeing. There's also a taxi stand and an airport bus pickup at the station. Lastly, the staff at Mimaru were especially helpful; they helped us untangle any challenges that arose (e.g. where to buy diapers in big packs, using Uber Eats in Tokyo, and how to book our bus tickets back to the airport).
We would absolutely book with Mimaru on future trips to Japan!