Position and prominence of 'Acknowledgements' in a publication
I generally make acknowledgements their own \section and place it at the end of the paper's body, before the references or any appendices.

But I really don't think it matters.  The referee is not going to care, and it won't affect the acceptance or rejection of the paper.  If the journal has a preference, you will hear about it from the copy editor when the time comes to correct the proofs.  

You might as well check the Instructions for Authors to see if it addresses this, but otherwise, just pick something reasonable and don't worry about it.