I live in Duluth, MN and am more familiar with the UP.  There are a number of good places to paddle there.  Sylvania Wilderness near Watersmeet is kind of a mini-BWCA.  The South Branch of the Ontonagon River in the western UP is a great 2-day river trip with some mild rapids along with a couple to be portaged.  It is canoeable most of the summer, although this year is probably really dry by now.  The Escanaba River near Lake Michigan is supposed to be nice.  A great book to check out is Canoeing Michigan Rivers by Jerry Denis.  This book also details rivers in lower Michigan.