Sister Bay has a fall fest one weekend in early October. We haven't been to that in about 2 years due to a change in my DD's school calendar.
Generally, the colors are beautiful at that time of year. If you are into hiking around, the Peninsula State Park is up there.
We would never go up there without visiting Hands On Art - which is a "pottery painting and other arts & crafts" studio. My DD loves this place.
The last time we were up there, one of the "outdoor theater" groups had started doing a play indoors which was fabulous, titled "The Bachelors". They were doing the plays near or at the city hall in Ephraim. I would definitely recommend trying to find out if a group is doing a play.
We always try to get to Al Johnson's - the restaurant with the goats on the roof.
My parents live in Sister Bay, so the only housing I am familiar with is their house. Sorry - I can't offer help with lodging.
It has been my limited experience that most shops are still open at this time of year, although if they are "closing for the season, there might be some good "customer appreciation sales" going on. Unfortunately for me - since my parents moved up there, they don't like to go out much when the "tourists" are in town, which limits our excursions. So, we really don't go up there much, because I don't want to drive 4.5 hours to go sit in their house.
Hope this helps!