As noted Duluth, MN (and Superior, WI) and Thunder Bay, ON on Lake Superior and Chicago and Milwaukee on Lake Michigan were (are) ports serving inland rail destinations. Chicago, serving everything to the South through the West, and bolstered by river/canal access to the Mississippi, is the largest. The others, serving farmland pretty much only to the West (and with no further serious water connections) are smaller.
Gary and Hammond (and East Chicago/Whiting and Burns Harbor), just to the South of Chicago provided some access to the South and Southeast, but were actually the result of a different accident of history: in the earliest days of iron mining in Michigan’s U.P., they provided a close point to process iron, where ships could make many runs per season along Lake Michigan, and coal (albeit soft coal) from southern Indiana and Illinois could be brought together fairly easily. (Initially, making a run from Escanaba to Gary was a couple day trip along Lake Michigan, while negotiating the St. Clair and Detroit Rivers added at least two days to a run to Cleveland.) Once the plants were established south of Chicago, they were maintained even after rail transportation and shipping each increased the transportation speeds.
The section of Ontario East of Lake Huron was not a significant exporter of produce (and it exported no ores) and much of what it did ship went overland to Toronto or London or Ottawa. And the limited amount of farming supplies shipped into the region followed the same paths. (Remember, Canada is still rather sparsely settled: Thunder Bay, at fewer than 150,000 people, is the single grain terminus for all of western Ontario, Manitoba, and Saskatchewan (with some input from Alberta).
The section of Michigan west of Lake Huron was, originally, an exporter of timber, floated out to the lake without need of ports, and even today is not a significant farming region. (The limestone handled by Alpena does not justify any large city.) Bay City acts as the port for Flint, Saginaw, and Midland, but only became significant after the rise of the automoblie and chemical industries, which arose too late to spur the development of many other ports besides the established Bay City.
In an alternative universe, I could see Lake Huron assuming greater importance. The earliest paths of the French traders actually ignored Lake Erie (with the horrendous portage past the Niagara Falls), coming up the Ottawa/Outaouais River from Montreal and portaging across to Lake Nipissing to Georgian Bay. If technology and history had developed differently (with, say, an Ottawa/Huron Canal preceding the development of steam and rail and the Brits holding on to Northern Michigan (and its iron and copper) after the 1790s, Lake Huron might, indeed, have developed a major city on its northeastern shore, but those are what-ifs that never happened.