Hi Cyndi,
What type of cottage are you looking for? Do you want to rent from a private owner or are you interested in renting a cottage that might offer more services (housekeeping, pool, etc). If you are looking to rent from a private owner, I am afraid I can't be of much help, but check out the websites others have mentioned.
Pictou Lodge is one option. It right on the water, has a private beach, a pool, restaurant and a variety of accomodations. Their website is www.pictoulodge.com.
Harbourside Cottages (www.harboursidecottages.com) would be another option. While there isn't a beach on site, there is a water view of a harbour. Melmerby Beach is about a 5 minute drive away. There is a pool there and the cottages are mostly 2 bedroom, all with kitchens.
Stonehame Chalets is a beautiful spot (www.stonehamechalets.com) with a great view. Though these cottages are not waterfront (Stonehame is on a mountain in Scotsburn, outside Pictou). They have 1-3 bedroom cottages with kitchens, a pool, and hiking trails. You would have a further drive to the beach (Caribou Beach would be closest).
There are other places along the Sunrise Trail you might want to look into as well, you can go to www.novascotia.com and search for cottages/cabins along the Northumberland shore for a full listing.
Hope that helps!