The largest impediment to a pre-eminent Midwest prior to 1900 is the concentration of power and early industrialist money in the east. As has already been stated much industry had moved or was moving to the Great Lakes by 1900 but the "Old Money," tradition, and center of political power remained in the east which prevented the new industrial giants of Midwest and Great Lakes from coming to fore.
With that in mind, what about a Reconstruction PoD where to better sow peace with the Southern states Congress agrees to move the national capital from Washington D.C.--a symbol of the Union but also, to the South, a symbol of Northern Tyranny--to a new location bereft of memories of the war. The location is hotly debated but it is agreed that it must meet several criteria: it must be more centrally located, needs existing rail and river access, and cannot be in a Northern State (doing so would just be moving the tyranny). Finally, St. Louis (or nearby) is selected. (EDIT: maybe Cairo at the confluence of the Mississippi and Ohio Rivers would be better?)
With the move of the nation's political center the wealthy industrialists and landowners also move their empires to be closer to the power. Since the south is still agrarian this means the nascent industry of the Great Lakes, the Upper Mississippi, as well as those of the Ohio River and other major tributaries become the business center of the nation, with the banks soon to follow.
St. Louis is a great capital for the United States, being rather near the center of the country while also keeping in mind the center of population of the country (and indeed, 1960 - 1990 the St. Louis metro area was indeed the center of population for the whole country). St. Louis is also a city which if it had better government, would have ended up a far better place even if Chicago would have always eclipsed it (an earlier POD could easily see St. Louis eclipse Chicago). With its position on the Mississippi and Missouri, St. Louis is IMO a pretty natural place to put a capital of a country like the US.
Although Cairo has better Southern credentials, it has the problem of needing massive levees and flood protection, since it's a fairly poor site as far as flooding goes. And besides, in 1870, Cairo had a population of about 6,000. St. Louis had over 310,000. The infrastructure is far better than in Cairo.
But if you moved the capital to St. Louis, although the area would remain far more vibrant (rather than the horrifying decay the area has seen, especially East St. Louis), I don't know how much the Midwest
as a whole would benefit, like Chicago, St. Louis's rival which in some ATL, St. Louis could easily have switched places with. Or especially places even further away like Detroit or Cleveland.
An earlier St. Lawrence Seaway might help, especially if there's no concerns with relationships between the US and Canada going south.
A really cynical, and perhaps unconstitutional, way to get the area doing well: Air Conditioners are declared a "Luxury, with possibly dangerous side effects," and SERIOUSLY taxed, and/or require yearly registration. This brings money into the federal coffers, and makes living in the south more expensive. Base the rate schedule on capacity to spread it out, or base it per unit to let businesses and the rich only pay for a handful of big units, while the less wealthy pay through the nose as they most likely, at first, can only afford window units, and not central air. Retrofitting central air is easy if a house has forced hot air heat--VERY difficult, comparatively, if it doesn't have ductwork.
The St. Lawrence Seaway would definitely be a huge benefit. IIRC, it was possible in the 19th century (which could be improved as the years went by), yet Anglo/Canadian-American relations weren't the best at the time and the British feared the Americans using it to gain control over Canada (this is why the Canadian canal network wasn't as good as it could be since it was feared the Americans might use the canals).
But regarding air conditioners, that almost does seem almost unconstitutional. And if not, just almost ASB for a movement to develop. Government regulation was nowhere near as powerful in the early 20th century as it has since become. I can't think of a single ground to regulate/restrict air conditioning that wouldn't also restrict a ton of other things. Maybe energy consumption? But wouldn't that not be a good thing, since it would increase coal prices, say? Or even the demand for a TVA-style project?
It's really difficult to do so because there are other lakes and harbours more useful than the great lakes. What you could do is stop manifest destiny, and have most rich landowners, especially rich landowners in the Deep South when rich enough move to the Great Lake states, and then Great lake cities like Detroit, or Chicago become the "Dubai" of America. You could also then have those rich people conducting the majority of business near ports, and the rivers. Foreign powers and Native tribes would use the Great Lakes as the hub of American trade.
But hey, at least I got those bonus points.
I'm admittedly ignorant on the subject, but how many great Southern landowners actually moved out of the South to become absentee landlords? I'd assume that if I'm one of the richest men in, say, Mississippi, based on wealth from my cotton plantations tended to by huge amounts of sharecroppers and their families, and I possess a great amount political control over at the very least my county (if not the state of Mississippi), why should I move to Chicago or Detroit where I have no means of political control aside from my wealth (i.e. I don't have my co nnections and networks there) and I'm probably not as wealthy as those Yankee industrialists.
Also IMO Manifest Destiny was inevitable given the demographics of the trans-Appalachian region (mostly empty) and the Thirteen Colonies (rather populous) as a united entity (the US). Once the trans-Appalachian region fell to the Americans, it's basically impossible to prevent at the very least the Mississippi Purchase area from being gained (since it was empty and the Plains Indians were living on borrowed time). But this kind of belongs in pre-1900. Take the earlier discussion of Duluth, Minnesota, for instance--Duluth in the United States doesn't have that much particularly special, but if you have an independent French Louisiana (or any other state with similar borders) which can get a Great Lakes border, then Duluth automatically becomes the best outlet to the Atlantic in this nation (which has huge amounts of potential) and thus will gain immensely as a result.