Besides being an urban plaza, the aptly named City Sq is also an archaeological site. Big Dig construction to reroute I-93 unearthed the foundation of a structure called the Great House, widely believed to be the home of Governor John Winthrop and the seat of government in 1630.

Winthrop soon moved across the Charles to the Shawmut Peninsula, and the Great House became the Three Cranes Tavern, as documented in 1635. Informative dioramas demonstrate the remains of the kitchen, the main hall and the wine cellar.