I spent ten lovely days on Grand Manan last July with my two kids and I highly recommend it! We stayed at the Castalia Marsh Retreat, which although quite "rustic" (i.e. compost toilets), has some great birding right on the property
http://www.castaliamarshretreat.com. There were two Bald Eagles to greet me each morning and the Nelson's Sparrows would often come very close to the deck. We took both the Whale Tour and the Puffin Tour with "SeaWatch Tours"
http://www.seawatchtours.com. Note that you are unlikely to see any whales on the puffin trip, and there is only a small chance of seeing a puffin on the whale trip (the two tours go in opposite directions), so you really want to do both. You should book the puffin tour as far in advance as possible since it usually sells out. For the whale trip, if you tell them you are birders they will bring a supply of chum to attract seabirds.
On a different trip several years ago we visited the Hopewell Rocks - worth the visit but not really an all day activity. Not too far away from there is Mary's Point, which I regrettably missed, but I hear it's the best place in the Maritimes to go for shorebirds. Are you planning to stay on the New Brunswick mainland as well? We stayed at a nice spot between Fundy National Park and the Hopewell Rocks called "An Artist's Garden"
http://www.anartistsgarden.com/index.htm. Sorry I've never been to Nova Scotia! Feel free to pm me if you want more details about Grand Manan.
-kris ito
