What do you guys like to do, and how far are you willing to go for a half-day trip?
If you stay in/near Boston, you have a lot of child-friendly places to stop into (the Aquarium, the Children's Museum, and the Science Museum are all very child-friendly, though expensive), plus parks with ducks and dogs and things, and for walks in the woods you've got lots of reservations and preserves within a half-hour to an hour. You can also day-trip to the North Shore and the South Shore and even to the Cape or Maine.
Western Massachusetts has lots of nice hiking/walking in the woods, some cute towns (Amherst and Northampton in the Pioneer Valley; various towns in the Berkshires), Six Flags, the Basketball Hall of Fame...
October can be very busy in the foliage-ish parts of New England (which could include Western Mass), but North Conway and Bartlett are very nice up New Hampshire; mostly there's walking in the woods, but there's also a small children's museum (more of a play space) and some downtown candy-shop areas.
Portsmouth, NH, Newburyport, MA, or somewhere on the southern coast of Maine (Wells, Ogunquit, or maybe Kennebunk) might also be good home bases - they're nice towns with easy access to highways so you can get to Boston, Maine, or New Hampshire within an hour. Plus October is shoulder/off-season around there so you might be able to stay someplace nice for cheap.
I also love Portland, ME, but I think it's probably more adult-oriented during the non-beach season (great food and cocktails... generally not of interest to 3-year-olds). It does have some child-friendly activities though.