Try Bragdon's Native People of Southern New England, 1500-1650 for a good introduction and overview. She followed that up with Native People of Southern New England, 1650–1775 if you want to follow the story a little further on after contact. I also highly recommend Lepore's The Name of War: King Philip's War and the Origins of American Identity for insight into how contact unfolded, and the factors influencing southern New England populations as the number of English migrants increased. Lepore's book is a little more academic, but still very readable, so I'd start with Bragdon. For an ecological perspective, you can't go wrong with Cronon's Changes in the Land: Indians, Colonists, and the Ecology of New England. The book dives into pre-contact ecology and land use patterns, and how that ecology fundamentally changed after contact. A great book.

Happy reading!