Hi again, HappyColor. You've gotten some great advice above. And, thank you for your very kind comments. I've worked in Boston for many years, so I know the city well.
I second poormom's recommendation of the Prudential Center Observatory, if you have time. Its official link is here
. A joke among the locals is that "the Pru" offers the best view of the city as it's the only view that does not include the Prudential Center Tower.
As to your questions...
1. Definitely include an interior visit to the main hall within Faneuil Hall. This is on the second floor... a Park Ranger can direct you. You might also find the Paul Revere House of interest, as it is the oldest residence in Boston (although no longer used as such). The Old Corner Bookstore is beautiful architecturally, yet this is certainly visible from the outside. I love its windows.
2. The walk between the USS Constitution and Union Oyster House isn't as easy as it looks on the map. I highly recommend a taxi between the two places. Yes, they'll take you.
3. Taxi between pier and Faneuil Hall will be around $10-$12. (I've done this a few times...) Make sure the driver turns on the meter. They are not permitted to charge a flat rate within the city of Boston. (Same goes for the trip in #2.)
Saving the best for last:
4. Yes to the Duck Tour. This will take you through several Boston neighborhoods, not just the historical ones. And, the portion on the Charles River will give you extraordinary views of our city and our sister city Cambridge... and also a great way to see the fall foliage. You can book this yourself (and take a taxi from the pier to the Prudential Center for around $20-$25) or through the ship (with pick-up at the pier). It's too bad the tour closest to the cruise shuttle drop-off point doesn't leave until 3:00 pm.
What time does your ship arrive and depart Boston?