Zurich has wonderful Zoo. The National Museum by the train station is nice. Check out the Museums in Berne, we took our Grandsons who loved it. Luzern has a Picasso Museum right downtown that is nice. If you take the boat trip in on Lake Zurich, get off at Rapperswil for a cool town to roam in. It has some restaurants by the docks and an ice cream shop.
Consider getting the Swiss Rail Pass. All trains, busses, trams, boats and most museums I mentioned are free. You activate it at the train station either at the airport if you go by train or the Zurich downtown station when you take your first trip.
Get Rick Steve's book on Switzerland for the names of the museum's as I know that I didn't provide accurate names for them.