Museon-Omniversum
Museon claims to be "the most fun-packed popular science museum in the Netherlands," and perhaps they're right. Permanent exhibitions center on the origin of the universe and evolution, nature, and the environment, with hands-on, interactive displays, frequent special exhibitions, and regular children's workshops.
The adjoining Omniversum "One Planet Dome" IMAX theater shows a rotating program of film spectaculars, mostly with nature-based and environmental themes, on a screen six stories high—your museum entry ticket includes one showing. For showings when the Museon is closed (separate tickets are sold), use the side entrance at Pres. Kennedylaan 5.
Museon-Omniversum is also right next door to the Kunstmuseum, so you can easily combine a visit to both.