We live in Moncton, New Brunswick, which would be right on your scenic route from Bangor to PEI.
Mid-September is very nice. You will see the beginning of the leaves turning. Maybe lean toward later September if your calendar will allow.
The drive from Bangor to PEI would be about 6 hours plus stops. You have a choice of two routes from Bangor to Moncton, and two routes from Moncton to PEI.
Bangor-Moncton (more scenic): State Route 9 to the border at Calais ME, then NB Rte 1 to Moncton. This is called the Airline (for apocryphal reasons). It will take you near beautiful Saint Andrews (but you'll have to exit off a few miles). You'll see the Bay of Fundy (and pass over the Reversing Falls in Saint John where the tides come in so high they actually push a rapids uphill).
Moncton-PEI (more scenic): NB Rte 15 to Shediac. After Shediac, get off the main highway and use NB Rtes 133, 950 and 955 to follow the Northumberland Strait coast all the way to the Confederation Bridge to PEI.
Bangor-Moncton (less scenic but easier drive): I-95 to Houlton Maine, then Trans-Canada Highway to Moncton. Four lanes the whole way. You'll see Mt Katahdin in Maine a way off in the distance, but otherwise its a dull road.
Moncton-PEI (less scenic but easier drive): Stay on NB Rte 15 all the way from Moncton, past Shediac, until you get to the Trans-Canada Highway again just before the Bridge.
If you fly to Halifax, then you would drive to the ferry at Caribou, Nova Scotia (near Pictou). The drive itself isn't much unless you use the parallel local highways, but the ferry is a nice ride.
I am surprised to hear flying direct to PEI from the US is even an option. I would have thought you would have to connect in Halifax. And if you do have to fly through Halifax, I would just as soon drive as connect. It won't take you much longer (maybe even faster, depending on the connection), and you'll have the scenery en route.