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You should consider both. Have a look at the trips on offer, prior to going, on the website. Invariably there will be tour companies on shore that do exactly what the ship will do, for a lot less money. The ships make great play about an independednt company giving you a problem if they don't get you back in time for the ship's departure time, leaving you stranded, but in reality, these companies are very slick at making sure you a) come back again & use them & b) recommend them. However, generally, the further away the tour is, or more involved/many faceted it is from the port your booked tour is, the better it is to go with the ship's.
We did this cruise on Sea Princess last year but we were a week or so later in leaving. I would totally agree with the other response you have received re using princess tours. Some are better value than others but the ship won't leave without you if you are late. Whilst in Boston we went up to Salem for the day and got delayed getting back to the ship but the ship waited. Highlights for us included Peggy's Cove in Halifax and Quebec. The weather varied greatly - sunny and warm in Newport, wet in Boston, cold in St Johns and even colder (-3C)up the Saguanay River! But we were lucky the sun came back out in Quebec and it was a bit warmer. But you will need to be prepared for all weathers and we even took gloves and a scarf. But last fall was generally wetter than normal so hopefully you will be a bit luckier going that little bit earlier. Disappointingly we missed out one of the highlights, Bar harbour, due to heavy seas. Have an great time!