Depending on where you are starting, you may consider a stop in St. Augustine, FL where there are fun activities for kids including St. Augustine Pirate & Treasure Museum and tours of the fort there. Savannah, GA is also a good stop along I-95 with great food and lots of beautiful parks. As you continue north, Williamsburg, VA has Colonial Williamsburg and also a Busch Gardens. Washington, DC is also a great stop with all the museums and monuments.
Oh boy, that's always an interesting drive with kids. I'm assuming you'll zip through Georgia to start. South Carolina and North Carolina tend to be long stretches of highway on I-95, so if you want to entertain the kids you need to be willing to take some small detours. South of the Border is the classic stop that everyone sees signs for on the highway. You could try Whirligig Park for a brief stop. Maybe eat at The Highway Diner. Once you hit Virginia, you could do Kings Dominion if you really want the kids to go crazy, or Lewis Ginter Botanical Garden for a more quiet stop. There's plenty of things in Washington, DC for kids, but that might be a trip in itself. Baltimore has the National Aquarium. Annie's Playground is a fun stop. Cross into Delaware and there's the Delaware Children's Museum. If you're staying in a hotel in New Jersey, check out the CoCo Key Water Resort. There are a few of these hotel/waterparks throughout the country. There's also Fun Station USA, and of course the Bronx Zoo, but you might want to get through NYC quickly or go around it possibly. In Connecticut, check out the Dinosaur State Park. That should pretty much get you to Boston!