Boston is the main urban setting for much of Assassin's Creed III's early sequence.
Assassin's Creed III begins in the American Colonies before shifting to the story of Ratonhnhaké:ton, also known as Connor. Boston is one of the game's two principal colonial cities and hosts major missions during the period leading into the American Revolution. Its streets, harbor, rooftops, and surrounding countryside form a substantial explorable area.
The game also includes New York City, the frontier, and several historical battlefields. Boston is especially important because the early chapters introduce the colonial conflict and feature events involving figures such as Samuel Adams, Paul Revere, and Benjamin Franklin.
New York City is a plausible alternative because it is another major playable city in the same game. Philadelphia and Charleston are historically relevant to the revolutionary era but are not the game's principal urban hubs. The question refers to the early sequence's main city, not every location in the campaign.