I absolutely loved Halifax and highly recommend the Maritime Museum, too. We did the "duck" ride and it was great! Good overview of the city and the harbor. We walked the boardwalk and had lunch at a restaurant, overlooking the harbour. We took a cab to the cemetary because we had extra time.
We also took the time to see the display right at the pier, there is a charge but it was well worth it! It was an excellent presentation about the immigrants coming to Canada.
I really would stay right in Halifax as it has so much to offer rather than doing a ship tour that takes you away from Halifax.
Bar Harbor has a great trolley that will take you to the National Park, its great fun and you do not need to book it through the cruise line. We got on just a couple of blocks from the dock area.
I really enjoyed the Vanderbilt estate in Newport but that is not everyone's cup of tea!
Boston has so much, you need to do your homework and see what interests you!