If you're talking inside 128, there are not many rivers or brooks that come to mind (at least ones that are stocked by the Division). About the closest I can think of are Stony Brook in Weston and Trout Brook in Dover. They also stock parts of the Charles, although mostly the upper reaches well away from Boston.
You have more options with ponds. Jamaica Pond in Jamaica Plain, Crystal Lake in Newton, Lexington Res., Houghton's Pond in Milton, Buckmaster Pond in Westwood, and Horn Pond in Woburn are all stocked, some heavily, and are relatively close to Boston.
Call 1-800-ASK-FISH for stocking info. They update it every Friday evening.
-bd