If you want to stay "somewhere a bit central and let papa take the train in to work", the place that immediately comes to mind is Shinjuku. That's really in a major urban center, plenty of convenient hotels at all points on the price spectrum and it's the starting point for the Odakyu train to Ikuta.

Another option would be to stay somewhere near Yoyogi Uehara - just a short distance out of central Tokyo, but significantly less hectic than Shinjuku and conveniently close to Yoyogi park, and some nice shops etc.. Unfortunately, I can't think of any hotels near there and I don't know if there are short-term rentals. It's possible that someone on this board knows of a possible place to stay around there.

You could also stay near any station on the Chiyoda line that runs through central Tokyo, since the Chiyoda line connects nicely with the Odakyu line at Yoyogi Uehara.