If you're starting in Saint John NB and have to leave by way of New Brunswick and you only have 5-7 days, it's probably best just to do New Brunswick and PEI. You could spend a couple of days on the Bay of Fundy in New Brunswick (including Fundy National Park), drive to PEI (Confederation Bridge), spend a few days in PEI, drive back to New Brunswick, and then head on your way. Depending on your route out of New Brunswick there may be some things to see and do along the way (I'm not very familiar with New Brunswick outside of the Bay of Fundy area).
There are lots of things to see and do in Nova Scotia so it might be best to do that as another trip. Also, if you're interested in visiting Newfoundland, ferries to/from Newfoundland run from North Sydney, Nova Scotia on Cape Breton. On my last trip in 2017 I flew into Halifax, visited Fortress of Louisbourg near Sydney, took the ferry to Newfoundland (Port-aux-Basques), visited western Newfoundland and also went over to Labrador for a day, took the ferry back to Nova Scotia, visited Cape Breton Highlands National Park, and then back to Halifax for the flight home.
On my 2007 trip I flew to St. John's Newfoundland and visited it, flew to Halifax, visited Cape Breton Highlands National Park, took the ferry to PEI, visited PEI, spent some time in New Brunswick on the Bay of Fundy, took the ferry to Nova Scotia, visited the Annapolis Valley, and back to Halifax for the flight home.