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Not sure if you are flying one airline for both segments, but you could inquire about checking your luggage all the way through to your destination which would eliminate the luggage issue.

From there, I would suggest taking the water shuttle from the airport to the Boston Harbor Hotel. It is a great way to take in the skyline and see parts of the city. From there you could get off the water shuttle and walk over Atlantic Avenue to Faneuil Hall Marketplace and see Faneuil Hall. There are good casual eating places or sit at the raw bar at the Union Oyster House, next to the Marketplace. From there you could walk through Haymarket, over to the North End and see the Old North Church and Paul Revere's House. From the North End, walk back up Atlantic Avenue towards the Aquarium and see the seals. Take the "T" from the Aquarium station back to the airport or continue up the street back to the Boston Harbor Hotel and get back on the water shuttle back to the airport. When you are on the water shuttle make sure you look over towards the Bunker Hill Monument and you will see the U.S. Constitution ("Old Ironsides"). You will need to take the Massport shuttle bus, which stops at every terminal to get to the water shuttle and the same for the return trip. Another option is to take the Silver Line to South Station and do the same walk up Atlantic Avenue past the Federal Reserve Bank, it is just a bit longer, but fine if the weather is nice. If you do that, make sure you stop by James Hook Lobster and visit the lobster tanks. They have one tank that has the jumbo lobster, which my son always loved.