Programming languages in computer science / applied math academic journals
I don't know anything about Computational Methods in Engineering or Computational Intelligence and Complexity, but I can speak to the other journals.  Journal of the ACM publishes plenty of theoretical papers, and the others you list are all mathematics or theoretical CS journals (although note that the American Mathematical Monthly is not really a research journal).  Papers in these journals won't generally include code samples, and you can write a theory paper analyzing an algorithm without implementing it.  If you do implement it, any reasonable choice of programming language is fine, whichever you prefer.  A computer algebra system can be a good choice for a proof of concept, but it's really up to you.

Incidentally, you've listed a rather broad range of journals.  It would be a rare paper that could comfortably fit into all of them, so you'll eventually have to narrow the field.  Based on your comments about code samples and implementations, I also wonder whether less theoretical journals might be a better fit, but of course it's hard to tell without knowing more about the paper you're writing.