Fairmont Battery Wharf on the Waterfront (from $219) opened its 150 rooms only last December ask for one with a water view. The patio opens in June.
Cook in your one-bedroom-apartment-style room at the Inn at St. Botolph (from $189). A sister property to XV Beacon, the inn opened in November 2008 as a low-key alternative on the border of South End and Back Bay.
Immerse yourself in the waterfront by booking a suite aboard the Green Turtle (from $245), a floating bed and breakfast. The tugboats churn the harbor by day, but the current is gentle at night.