Is the PNG file format acceptable for academic papers?
Running a journal with Wiley as a publisher, Wiley's instructions state JPEG, TIFF and EPS are acceptable formats. Since many authors supply figures in PDF and PNG I started to pass these on to the type-setter and found that no issues erupted. It is therefore clear that publishers may lag behind with their recommendations while type-setters are quicker to adapt to "new" formats. I imagine the lag is possibly a lack of interest to update what works, but can also be because they work with many type-setters and printers and wish to maintain a largest common set of files that they know all can accept rather than having to constantly adapt to individual services' capabilities. I am fully aware that this thinking is a bit arcane and that any type-setter/printer that cannot handle almost everything has very little potential for survival in today's competitive world.

Anyway. I would suggest asking the journal if it is possible to use PNG in your case, or do as many authors have done in "my" journal, send them in anyway. It may, for example, be possible to send in a JPG and a PNG copy of the graphics asking them to use the PNG if possible. 

As a side point: PNG is in my opinion the best pixel format because of its strong loss-less compression except for photographs, something it was never intended for anyway. Using PNG graphics will keep down the size of final PDFs of the article which is a good goal to have. So in my case, I encourage authors to provide PNG even though Wiley does not.