I'm the family cruise editor here. My 8 year old daughter has been on 10 cruises so she's well traveled. I took her on a N.England/Canada cruise when she was 6-/12. She enjoyed it but she was old enough to go to museums, etc. THere really aren't any beaches for little ones. I'd suggest holding off on that itinerary until your children are a few years older. In Halifax, we toured the citadel fortress, went to a museum and walked through the public gardens, and shopped. In St. John, we took a full day tour to see some of the small coastal towns and a small beach in N.B. It was lovely but I wouldn't suggest that tour with young ones. St. John itself is okay but there's not too much to do there especially with children.
I think Bermuda, Caribbean and BAhamas are better destinations for pre-schoolers.
Keep me posted what you decide.
We have cruised to Canada twice with our children. Our ship however did not make it to St Johns. In Halifax there are the Gardens. They are historical and beautiful. Its a nice walk to take. Also, I suggest hiring a taxi to take you to Peggys Cove. It is absolutly beautiful!! If you hire a taxi you can get a personal tour of Halifax and its fun. I almost forgot about the Citidel. There is a lot of history there, they have the changing of the guards, the bagpipes and Its the highest point in Halifax, you can see the ship from there. Another thing, if you are members of AAA you might want to get the Canada book from them and you can get a good idea of things to do. The tours offered by the cruise lines are very $$$$$ . Just a suggestion - bring light jackets. We were in Canada in June and in Auguse and it was chilly both times!! Have fun!!!!!