J.B.
I agree with Maria M. I would park somewhere near the waterfront/Faneuil Hall. It might set you back $30 but you'll have access to so much. The forecast for Sunday is perfect for walking around. That area has Faneuil Hall/Quincy Market, where there is all kinds of shopping and people watching. A zillion restaurants. You can walk right to the waterfront now too. The Big Dig took down a highway that used to cut off the waterfront from the rest of the city and that whole area is a series of parks. We often head in, park, and then just walk the parks - you can grab a bite to eat and go find a table in the park to have lunch at, bring a football or frisbee and have a pass in the grass, walk to the North End for a cannoli at Mike's Pastry, etc. The parks stretch from Chinatown to the North End and put it all in walking distance. That part of town is really easy to get in and out of if you're driving too - the highway runs right underneath you along the water so you just follow the signs on and off the highway.
If you want to go a little further into town, you can park at the Boston Common garage and there's lot's to do there as well. You can walk over one of the foot bridges to the Esplanade and hang out on the Charles River, go window shopping on Newbury St., grab a bite to eat, see the State House and Beacon Hill, walk through Boston Common and the Public Garden, etc. I think that this area is more geared towards adults who enjoy architecture and landscaping though - with a son the age of yours, I think that the first location mentioned would be more fun.