We just returned from the 5-day New York to Maritime Canada cruise on the Victory (7/26/03 sailing) and had the most amazing time!!
Weather in that region is incredibly unpredictable. Your experience in early September might be quite different than ours in late July, of course, but the day before our sailing, I checked the weather in Saint John and Halifax and it looked as though it would be about 65 degrees and rainy/foggy.
However, we had absolutely idyllic weather the entire cruise!!! Never a drop of rain, temperature hovering around 75 degrees, no humidity, cloudless, sunny skies! We were so thrilled with the gorgeous weather, and hope you are similarly blessed! I'm very jealous that you get two extra days, of course. :-)
The ship definitely rocked a bit during our cruise. Waves were considered moderate and 4.5-7 meters (gotta love the Captain's Log on the stateroom TV!) on average, and it was actually a little rougher than I'm used to the first night out of New York. After the first night, though, I got used to it, and grew to enjoy the motion and gentle rocking, especially at bedtime. After that first night, I did not hear any other passengers complain about the ship's motion. The trip back from Halifax was actually quite smooth and gentle, with calm seas and wave heights of 0-3 meters. Check the Captain's Log every day and you'll know what to expect. :-)
You will absolutely love your cruise, and the Victory is our favorite ship so far! Halifax is an especially interesting and beautiful city. I would like to recommend Bob MacLintock's "Tour by Taxi" instead of a Carnival shore excursion. We took his four-hour tour of Halifax and Peggy's Cove for US$140.00 total, and travelling with a private guide is soooooo much more comfortable and relaxing than sitting on a tour bus, in my opinion. Also, Bob is so knowledgeable about Halifax, and is an amazing guide. He took us to two gorgeous, small fishing communities on the way to Peggy's Cove that no bus could ever get to. He allowed us plenty of time to take photographs and wander, and dropped us off at the Halifax Public Gardens, which is a wonderful, serene way to end your tour of this beautiful, cosmopolitan city. Here's his website if you are interested; tell him Jen and Pete from Cincinnati sent you if you decide to use him!
Have a wonderful cruise!!!!