Great advice, Javert. Allow me to add some more info.
Martha's Vineyard: No need for an organized excursion here. There's a public transportation system (click
HERE) that covers most of the island. Just make sure you leave enough time to tender back to the ship.
Boston: If you feel like walking, the Freedom Trail is a good choice. Take a taxi from the pier to the Information Center on Boston Common, where you can pick up a map.
Halifax: I've only done Peggy's Cove through a ship's tour due to its distance from the pier in Halifax. If you want to stay in the city, I agree that the Citadel is well worth seeing. Other choices within walking distance of the ship are the Maritme Museum and Pier 21 Museum.
Regarding the taxi at the end of the cruise, the street you'll be crossing is 12th Avenue. The pier is on one side of the street, and a taxi stand is on the other, pretty much directly across the street. Do NOT accept a ride from a driver offering one while you are still inside the terminal building. It's also possible to get a taxi right at the terminal exit, but if there is more than one ship in port, this becomes very hectic and you may have a long wait (as in 45 minutes to an hour). I'd check there first, and if it's too crowded, take the elevator to street level (the taxi area is at the top of a ramp) where you can find a taxi much more quickly. If there are none at the taxi stand, just hail one...we've never waited more than a few minutes. Of course, it also means bringing your luggage with you...something else to consider.