Many thanks to www.Bostonsnewwaterfront.com and Lauren Grymek for this comprehensive information on multimodal navigation of the waterfront and Boston Harbor! Take the Silver Line to the Courthouse station and visit the Institution of Contemporary Art. Rent a Hubway bicycle (don't forget your helmet!) and ride along the HarborWalk to the New England Aquarium.
Stroll through Christopher Columbus park to the North End for lunch before picking up the Freedom Trail and visiting Old Ironsides in the Charlestown Navy Yard National Historic Park. Rest your tired feet by taking the MBTA Inner Harbor Ferry back to the Aquarium, or call a water taxi to take you back to the dock of your choice. Not done yet? Take a harbor ferry out to Spectacle Island for a sunset clambake on the beach!