Hamamatsu Science Museum is a good rainy-day stop, especially with children. Its hands-on exhibits are split across nature, space, sound, light, and electricity, so the museum feels more like a place to try things than a row of display cases.
The planetarium on the third floor is the main reason to allow extra time. Pair it with the nearby Museum of Musical Instruments if you want a full indoor afternoon in central Hamamatsu.