Those of us who live up here (I'm in Ellsworth), pretty much stay away from the island during the summer. If i wanted to sit in traffic, I would have stayed in NJ.
Any place like Northeast or Southwest are very expensive! ...and more so in the summer.
You can get some of the Acadia experience by going further Downeast to Schoodic Peninsula. WAY fewer people and just as beautiful.
If you want to do a whale watch, try to go with Allied Whale Watch. They are associated with the College of The Atlantic and they are out for the whole day. Their main reason for being out there is whale research and you are along to help pay for that research.... whereas the other whale watching businesses are there solely for the purpose of getting your money. You go out for half a day and they sell you the food and drink. You bring your own with Allied but I'd rather help support research then someones pocket book.
One can rent rooms in Ellsworth or along the way to the island for less then on the island.
For puffin watches, you'll need to check out this place:http://www.boldcoast.com/msi.htm
Machias Seal Island where you get to go out on the island and sit in little buildings that look like 3 seater outhouses and the puffins are all around you. You open a little window and point your camera and shoot away!!
Way more stuff to do up here than just the big island!!