There were no real flying craft at the time, except for balloons. The news articles of the day described self-propelled metallic aircraft.
The Mississippi river drainage is huge. But a flying craft would have been difficult to miss as it would have been unique and startling to observers of the time and the same craft could have been seem by many from different vantages.
Steam-driven trains from that time are known to have traveled a couple hundred miles overnight on flat prairie land. No reason a space craft couldn’t have explored the primitive industrialized areas of the Midwest in the 19th century and be easily seen.
After all, what did the aliens have to fear; we didn’t have deadly rockets or missiles at that time in our history. The atomic bomb changed all that.