There’s the Museum of Modern Art in Saitama, but if you are into bonsai, then I would have thought that the trip was well worth your time as the neighbourhood gardens and the commercial nurseries can be visited also.
If you have an interest in civil engineering, then you can enquire about a tour of the Metropolitan Area Outer Underground Discharge Channel near Minami Sakura station. I’m looking to pay a visit when my kid is a bit older.
Anyway, that’s my “visit Omiya” itinerary. Haven’t managed to go yet, but my husband has worked at the Museum of Modern Art and recommends it highly.