If you are going to Chicago you could consider deviating from the NT route by taking the rail-trails through Wisconsin. Active trans sells a Chicago cycling map here: http://www.activetrans.org/shop
If you are going to downtown Chicago you could take the Lakeshore path towards Milwaukee. There is a lengthy trail running from Waukesha (just west of Milwaukee), WI to Cottage Grove, WI (just east of Madison). If you are heading to the western suburubs of Chicago then you could make your way towards the Jane Adams Trial, which joins up with the Badger State Trail in Wisconsin, and takes you into Madison. These are generally crushed limestone trails, unless you are near a major urban area, then they are paved.
Heading out of Madison I know a back-roads route to Devil's Lake State Park, and from there it is a short ride to pick up a network of trails that will take to La Crosse, where you could rejoin the Northern Tier route. There are also more miles of bike paths on the Wisconsin side of the Missippi (again, generally crushed limestone), so you could continue north and rejoin the NT route at a later point if you chose. Options would be the bridge at Winona, MN, or you could stay on the east side of the Missippi and rejoin the route just north of Red Wing, MN.
Madison has a large Farmer's Market on the Capitol square every Saturday morning, and smaller markets elsewhere in the city on Wednesdays, Sundays and Saturdays. There are many organic suppliers and farms, and I believe some of them are within an easy ride of the route I've described above. I'd have to do more specific research. There is also a local/organic specialty grocery store in tiny Paoli, which is near the Badger State trail a few miles south of Madison.
I'm an advocate for Wisconsin cycling, obviously. Compared to Illinois and Iowa you will generally find a lot more trees, hills and bike trails. I grew up in Iowa, so I'm only biased against Illinois.
The scenery in western Wisconsin near La Crosse is truly stunning.