When is it appropriate to wrap text around an image in a scientific paper?
This is going to largely depend on the style guides of the journal(s) in question. If your long and tall figures are the best way to display the image, wrapping text around them is one feasible solution. The editors of the journal will be able to best guide you on this.

I would submit the manuscript in a clean and readable format, then let the editors decide how they want to format your graphic. I have never heard of a journal rejecting a paper solely because the graphics where of unusual dimensions.