The Wenham Museum on Boston's North Shore is a great family-oriented museum. It is a 45-minute drive from Boston on weekends. They have several compelling permanent installations - of substantial doll and model train collections and a historic home - as well as fresh exhibitions. A recent one on firefighting had an area where kids could try on firefighter gear and play, which was great on a rainy day. They also have many special events that are always tempting. My 5-year-old daughter and I attended a World War II event last summer where she explored the world that her American Girl doll Molly lived in by seeing real WWII materials up close (a carrier pigeon cage, men in uniforms, etc.). They have a space for workshops inside.  There's also a nice gift shop with many old-fashioned toys.