We did a very similar itinerary, but went to Portland instead of Newport.
We absolutely LOVE Bar Harbor! Such a wonderfully quaint NE coastal town. We did a HOHO bus and went up to Cadillac Mountain. Great way to get around and see the area. Great restaurants with amazing lobster lunches!
Halifax is also wonderful. We went to the brewery for a tour, which was awesome and then went to the Citadel, which is very interesting and educational. Great walk along the waterfront.
St. John has some good shopping and very good restaurants. We rented a taxi with another couple and just had him take us around the city to see the sights, including the Bay of Fundy, which is a unique natural phenomenon.
We also did the HOHO bus in Boston and thought this was a fantastic way to see the city. There are a couple to choose from and there are street vendors selling tickets. Strange how the price changes between the vendors and the bus companies themselves. Do some homework beforehand to find the one that matches your needs and check out the prices. Then wait till you get into the city and talk to some of the street vendors as you'll get a better deal. But this is definitely the way to sightsee around the city.
When we were there (late September) the leaves were changing and the entire area was bathed in beautiful Fall colors. We thoroughly loved it and would do it again.
Just make sure you take layers. We had rain jackets and sweaters so if it was rainy and cool, we would wear both. Or if it was just cool and dry, then we had the sweaters. When we first arrived in Portland, it was raining very hard. Luckily, as the day went on, it dried up so it did not ruin the whole day. But we had a couple of days where it was misty and cool, which is not unusual for the area in the Fall, so just be prepared.