Mid September into early October is beautiful. We usually go to the Ely area the last week of September. The colors are generally peaking at that time. During the day you may see a few flies if warms up enough 50-65 during the day. Night time gets into the low 30's mid 20's.
Keep in mind the small game hunting season opens around September 15th. You may run into some Grouse hunters on trails. Not a big deal but you might want to wear a blaze orange hat.
The shuttle runs weekends from mid-May to mid-October. It's best to leave your car, ride the shuttle, and hike back to your car.
Earlier in the year is better for water in the small streams but you'll come to a good water source a few times each day.
I live in Finland and that has some nice sections of trail but anything south of Grand Marais is beautiful.
And yes there are bears on the trail, I've seen them. Hang your food away from camp and you shouldn't have a problem though.