Massachusetts' official website (mass.gov) lists 61 different places to go kayaking and canoeing in the state, including (but not limited to) 25 state parks, 16 state forests, the Boston Harbor Islands, the Charles River, and Pope John Paul II Park in Dorchester.
("Pope Park" was founded in 2001 and is appropriately named — Pope John Paul II was an avid outdoorsman. As a priest in Poland, he often took paddling trips and held mass outdoors. During these trips, he would occasionally use an overturned kayak as the altar, and the oars as a makeshift cross.)
Just north of Boston, in Newburyport, you can go kayaking with seals.