You don't want to stay "downtown" - and there's nothing to do downtown, except the National Museum of Play, and you can easily just drive to that.
The apple orchards are, of course, outside of town, out in the suburbs and farms. Some of the farms have "maize" mazes that kids might like, along with various other activities. Powers Farm Market sets up a big tent for October with pumpkins, etc. Schutt's farm has apple cider and apples - not sure whether they offer tours of apple fields or not.
The Delmonte Hotel mentioned by another poster is actually in Pittsford, which is a cute little town, as is Fairport. Not sure that hotel is particularly "kid-friendly", as it's pretty upscale. Both Pittsford and Fairport are right on the canal and will likely have family activities in the Fall. You can take boat rides on the canal, walk/bike along the canal path, etc.
You will definitely need a car to get around in Rochester. The type of sights you mention are not centrally located and are not in Rochester itself.
Other activities you might be interested in: Rochester Museum and Science Center; Genesee Country Village; WIndmill Farm market [Saturdays only, and it's about 1.5 hrs from Rochester, near Penn Yan, in the beautiful Finger Lakes].
I would guess that you could find more suggestions by doing a search on "Rochester tourism" or something similar.