In lines 87-90, Mann writes that "new England's major river valleys ... held large, permanent villages, many nestled in constellation of suburban hamlets and hunting camps." What words in this sentence have strong connotations?

I would say that "large, permanent villages, many nestled in constellation of suburban hamlets" has connotations of being a well-settled area, well established and the "nestled" connotes a comfortable arrangement and in a "constellation of suburban hamlets" indicates a large series of "suburban hamlets" ie what sounds like the beginnings of cities.