Her husband, Thomas McGuinness, was co-pilot of American Airlines Flight 11, which was flown into the World Trade Center's North Tower.
The 7,800-ton, 337-foot submarine was built by General Dynamic's Electric Boat and Northrop Grumman Shipbuilding.
"She's a living, breathing soul who will provide a home to her crew," said Representative Joe Courtney, a Democrat from Connecticut.
The Navy said the submarine, which will have a crew of about 134, is an example of technology efficiencies and budget advances. It was delivered $54 million under budget and eight months ahead of schedule, the Navy said.
Scores of onlookers, including officials of the Navy, members of Congress, and Electric Boat workers helped celebrate the christening at the Electric Boat shipyard.
The submarine is scheduled to begin sea trials this summer and is scheduled for delivery to the Navy in October at a ceremony at the Naval shipyard in Kittery, Maine.