I'd save the puffin tour for when you go to Newfoundland. Cape Breton has some interesting spots but the drive is not all that interesting. My all-time favorite place on Cape Breton is The Normaway Inn, 691 Egypt Rd, Margaree Valley. It is a lovely area - beautiful river, great food and great musicians. It's not on the coast and it is very special. There is a big old hotel, Keltic Lodge, on the east shore of northern Cape Breton that might be interesting as well. I stayed there and it's expensive but has an excellent location if you like the sea. The Alexander Graham Bell National Site is worth a visit.
I have to disagree about the drive! It's quite stunning and if you are into coastal drives there aren't many nicer places than the Cabot Trail to go.
I do agree that there are some hidden gems off the main loops through Cape Breton and the mainland and I encourage you to go explore off of the main highway when possible.