I'd definitely recommend the South Shore, Lunenburg is a UNESCO world heritage site (for the old town), docks, harbour, lots of fixed up old victorian houses, etc. Lunenburg academy is incredible. Take the short drive out to blue rocks for a much less touristy fishing village look that will be all but deserted compared to Peggy's Cove (and a different type of rock too). Peggy's Cove is beautiful but that entire area of coast is great and Peggy's Cove is the one area that gets all the "cred", go to Indian Harbour (not far from there) and see the same stuff with no tour busses, or Prospect, or Chester, etc, etc.
If you're hitting Lunenburg then also take some time in Mahone Bay which is also quite beautiful.
I'm a little biased for the South Shore because my family's from there.
For Halifax (my locale, feel free to get in touch for a coffee or something) the waterfront and harbour is nice. If you're on foot, take the ferry over to Dartmouth for a great view of the city (really nice at night and the cheapest "harbour cruise" you'll ever find at $2 each way), citadel hill and the forts at point pleasant park can be worth a look. If you have the time and are interested in forts then take the time to head out Purcell's Cove Rd. to York Redoubt which isn't as visited and has a lot more fortifications (all part of the harbour defences which were active up to WWII in some cases).
Other sites, maybe head to the Annapolis Valley for a different thing, Annapolis Royal is really nice but it's been ages since I've been there. For Cape Breton, it's hard to go wrong wit the Cabot Trail and Louisburg.
Again, feel free to drop me a line for more info or to grab a coffee.