There are two schools of thought concerning shore excursions; book through the cruise line or book independently.
If you book through the cruise line, people will say it's more secure and they guarantee you won't miss the ship. However, these excursions are usually more expensive, more regimented, less enjoyable, and always more crowded.
If you book independently, people will say it's less secure and there's no guarantees you won't miss the ship if something happens. But there are different ways to book independently; one is to simply do you own thing - rent a car, hire a taxi, take public transportation, etc. Or you can book it with an independent company, such as Shore Trips (there are many others - I'm just using them as an example). Good thing about booking with a large company like this is that they guarantee you won't miss the ship and if, on the off-chance you do, they'll pay to get you to the next port of call. However, as Julie Karp, President of Shore Trips, likes to point out, in the tens of thousands of shore excursions they've booked for people, no one has ever missed the ship. Excursions like this are sometimes the same price and sometimes cheaper, but they are not as regimented, more enjoyable, and always less crowded. We've been doing them for years and in 45 cruises have never had any problems.
Now, with that said, during your Canada/New England cruise is different than going to 'foreign' countries. The ports are wonderful and there are some great options for you. For example, if you're going to Bar Harbor, which is one of our favorite ports up there, you can do the Hop On Hop Off bus and see what you want to see. It'll definitely save you money over any excursions offered by the cruise line. You can do the same thing in Boston and it's a great way to see the city. Halifax is awesome and easy to get around - definitely suggest going to see the Citadel.
We loved our Canada/New England cruise and hopefully we'll get the chance to do it again sometime. Wonderful ports, awesome seafood, great sightseeing, and terrific people!