Stayed in Seacliffe B&B in Brigus in July. Beautiful. Not sure what your budget is, this is a brand new B&B 4+star. Brigus is about 1 hour from St. John's, small, quiet town, beautiful view, museums. Or, Witless Bay has the Bear Cove Inn which was also very nice, but not right on the water. Neither are cottages, but thought it might help.

We stayed at Pirate's Peek in St. Philip's last summer and loved it. It was a house, so has a nice large kitchen and living room, all very well appointed. The only thing is that it has 3 bedrooms, one master and two smaller ones.