I've never stayed at any of the three. But here's a few things: The Manor House Inn has the nicest location, across from the water, set back from the street, with pretty grounds. Really easy walk to restaurants, shops, and boat tours. On the other hand, there is cruise ship bus traffic on the street where the Manor House is located. And the very large and bustling Harborside Hotel and Bar Harbor Club is across the street.
The Elmhurst Inn recently changed hands. They changed the name from Greycote Inn. That's why you don't see as many reviews of the Elmhurst as you do the others. The Elmhurst is a few blocks further from the center of town than the other two. It's on a somewhat quiet side street, compared to the other two. However, the town grocery store is near the back of the inn, with the noise of delivery trucks. Also the town hardware store is almost right across the street.
Stone Throw Cottage is set nicely back from the street with a good parking area and a lovely front lawn, complete with three story lilac tree. I've heard the bathrooms have beautiful painted sinks. I've met the owners and they are truly gracious. The walk to Main Street from Stone Throw is easy and also very pretty, past churches, library, and the Village Green.
I think all three are great inns and Bonnie summed up their pros and cons excellently!
Depending on what you want to do on the porch, I think the Stone Throw or Manor House may be better for people watching; the Elmhurst may be quieter for sleeping. Stone Throw also has an amazing large back yard filled with flowers if you're looking for a quiet spot.