I'll tell you what I know based on our annual visits to Bar Harbor/Acadia. While we visited in June this year, we have visited in September in the previous 8 years.
First off, the Puffins are all out on the open seas now. We saw them out there on the Maine Audubon Pelagic Trip out of Bar Harbor last year. They are nesting on islands like Machias Seal Island in the May-July time frame. The reason we went in June this year was to see the Puffins on Machias Seal Island.
Second, I have never found that area of Maine to be good for shorebirds primarily because there isn't much shore. Most of the DOwneast coast is very rocky and rugged. There are precious few very small beaches for shorebirds in the area.
That's the bad news. The good news is that I think the Schoodic Peninsula (part of Acadia on the next peninsula up from Bar Harbor) should still be good then. There should still be tons of Eiders (Common and if lucky you might find a King mixed in). The loons should be moving from the inland lakes and ponds to the coastal ocean areas. We photographed Peregrines over on Schoodic. Also saw some Murre and Guillimots from the rock cliffs along the Ocean Drive Trail in Acadia.
Ed, thanks for sharing the info. Like Michael, I too am going there in mid-October (9th through 19th) and will be staying on Cadillac Mountain. Other than the obvious places there in Acadia, do you, or anyone for that matter, have any other suggestions for places in the general area...for landscapes, waterfalls or birding?