We absolutely loved our Canada/New England cruise!
We have never left out of the Brooklyn pier, so I can't help you with that one.
We also didn't do Newport - we did Portland instead, so I'm not any help on this port.
The pier in Boston is a ways from downtown, but there's a shuttle bus (for a fee) that takes you there, then you can walk around or do whatever. We did the Hop-On/Hop-Off bus and it was a great way to see the city. We got off at several stops and saw various things we wanted to see; the USS Constitution, Paul Revere's house, North Church, etc. There are a couple of different companies you can use and they will all have people walking around the downtown area wanting to sell you tickets - just find the best price and go for it.
Bar Harbor was one of our favorite ports - absolutely wonderful! But the ship does not dock, so you'll be taken to port by tenders. Once there, you can walk everywhere. Some awesome restaurants - we found one and had 2-1/2 pound lobsters for lunch!! We did the HOHO bus and went up to Cadillac Mountain.
Not much to do in St. John. You can walk off the ship and do some shopping and sightseeing. We did find a nice restaurant and enjoyed some great food.
Halifax was another favorite port. Again, you can walk off the ship and sightsee or shop. We went to the Alexander Keith's Brewery, which was really nice. Then we saw the Citadel, which was very interesting. And again, we enjoyed a wonderful lobster lunch.
There are excursions available in every port, but I highly suggest not doing them through the cruise line - too expensive, too crowded, and too regimented. We much prefer to do our own thing or get excursions through independent companies, which are usually cheaper, alot less crowded, more fun, and more intimate. Plus, they are usually very accommodating and flexible.