if you can spare time to be with your son on a weekday, the Minuteman is generally quiet outside the standard commuting hours, though I agree that it can be a zoo on the weekends.
Similarly, if you can square the time to get out to the Middlesex Fells on a weekday, you have the option of doing both mountain biking trips and just nature walks in the outdoors. On a weekend, though, the mountain bike loop is also pretty crowded.
Otherwise, you could look at the Fresh Pond Bike Path. That tends to be the least trafficked of all of the local bike paths, as it's relatively out of the way and its utility as a commuter artery is limited.