I assume you are driving. In that case, take route 1 or 1A though Maine (beautiful scenery). From Eastport, you can take a bridge to Campobello Island (NB) and visit the former Franklin D. Roosevelt summer home, then take a ferry to Deer Island, then a ferry to the NB mainland. Or you could skip Campobello and drive to Calais. Alternatively, exit I-95 at Bangor and take route 9 to Calais where you cross over to St. Stephen, NB.

From St. Stephen to Saint John is less than 90 mins. Along the way you should visit St. Andrews, a town settled by Loyalists more than 200 years ago. There a a number of B&B's, pubs/cafes and a very nice Fairmont Hotel, the Algonquin.

Please very very careful to write and say Saint John (NB) rather than St. John's (which is in Newfoundland). I grew up in YSJ and the natives are very sensitive about the name of their city. YSJ is a convenient place for visiting Fundy.
West side of the city: Irving Nature Park (sticks into the bay), Carleton Martello Tower.
Downtown: Loyalist House, City Market, NB Museum, King Square, Loyalist Burial Grounds, Trinity Church, Jewish Museum, Old Court House, Harbour Trail.
North: Reversing Falls, NB Museum (main location), Fort Howe, UNB, Tucker Park Beach.
East: drive past Red Head and Mispec Beach to Cape Spencer Lighthouse. You may see whales or dolphins (but nothing else). Drive past the airport to St. Martins, an old shipbuilding Community. Walk the beach, buy a painting, have lunch. From St. Martins, you can drive the "Fundy Trail". From St. Martins, you can return to YSJ or drive to Sussex on your way to Moncton.

YSJ Accommodation: Hilton and Delta are both right downtown. There are a range of mid/lower tier chain hotels scattered around the city.

YSJ to Moncton (YQM): east of Sussex, follow the signs for Fundy National Park. The village of Alma services the park and right on the edge of the Bay of Fundy. From Alma, it is 45 mins of so to Hopewell Rocks. From there 30-40 mins to YQM.

As I'm from YSJ, YQM has never held that much appeal for me, however there is a wide range of accommodation and dining options... or you could drive 30 mins to Shediac on the Northumberland Strait. Parlee Beach. From either Moncton or Shediac, you can be at the Confederation Bridge in less than one hour via the TransCanada Highway. From there, PEI is directly in front of you... or actually a bit to the right. Warning: make sure you have accommodation reserved in advance for PEI, or do a day trip from Moncton.

PEI: Charlottetown, Anne of Green Gables, Cavendish, lobster, beach. Shame on me for being so concise about Canada's smallest province, but that's all you will have time for.

If you have any specific questions, lemme know.
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13F

PS Sorry Fredericton.