Here's the link to the free transportation for Downtown Halifax, sometimes they even have a tour guide on board the bus. Best priced
cruising excursion to be found anywhere
http://www.halifax.ca/metrotransit/fred.html
Now to clarify the St. John's/Saint John confusion found here.
In Atlantic Canada we have the two Cities.
Saint John (note we don't abbreviate for Saint) is in the province of
New Brunswick, it tends to be the Port, besides Halifax, that most of the 4-5 day Cruises out of Boston and New York visit. It's a nice, on the smallish side, Industrial type city. Has a great City Market, maybe 10-15 minute walk from your Ship. The Great thing is you can get there by going through pedways and a couple of Malls.
St. John's is in the province of
Newfoundland, you probably won't see it on a 4-5 day cruise out of Boston/New York. On a longer Cruise you might see it, even some Trans-Atlantic Cruises stop over.
I haven't been to St. Johns, but from what I've heard it's more of a Government/Educational type City.
Oh well, since I'm on a roll

Halifax is the biggest city of the three.
Large Military/Government presence, numerous Universities (Dalhousieand Saint Mary's the two biggest schools). As I mentioned earlier about the Free Bus service. It goes to all the downtown tourist atractions
Maritime Museum, Citadel Hill, Public Garden, Casino etc. To take you time and visit all the attractions it stops at you would need more than one day. The best part about it it's free and it stops right at your Ship. Here's the map of Freds last year route.
http://www.downtownhalifax.ns.ca/images/Fred%20Map.pdf
Lots of Tours can be booked right on the waterfront, you don't need the transportation that the over priced Ship excursions charge you for.
I you have any questions about Halifax, or Saint John jusk ask. As for St. John's I'm going there later this month and will better prepared to answer questions about it when I get back

.
Have a Great Day!