We visited New Brunswick and Nova Scotia during the first three weeks of June back in 2008. Would have stayed longer, but had to get back to attend a wedding. Our main goals for the trip were to see the tides in the Bay of Fundy and to explore around Cape Breton Island. We thought we would include a visit to Prince Edward Island, but ran out of time.
If you haven't been to Acadia National Park on Mt Desert Island in Maine, you could plan on 2-4 days there.
We crossed the border at Calais/St Stephen. We spent several days at Century Farm Campground in St. Martin NB to explore the nearby area. The Fundy Trail Parkway was interesting as well as several covered bridges and seeing the boats sitting in the mud at low tide.
We also spent several days camping at Fundy NP and did several hikes.
IMO the best place to experience the Fundy tides is at Hopewell Rocks PP. We were lucky and got there just at high tide and stayed to explore the visitor center and have lunch before going back to walk on the ocean floor among the teapot rocks while the tide was out.
From Moncton we drove across to Cape Breton Island and did a clockwise loop up to and around Cape Breton Highlands NP. Some steep grades in the NP, so doing it with the toad is recommended. We camped 2 nights in Baddeck to visit the Alexander Graham Bell museum then drove to Louisborg for two nights to visit the Fort reconstruction. Definitely a highlight of the trip. From there we worked out way to Digby for a Scallop dinner and took the ferry ($$$) to St. John and headed for home.
Don't know whether this is much help to you as we tend to travel by "wandering around" without any fixed plans or advance reservations.