By both those references, it's "URLs",
not "URL's".
rubyrescue: since you're posting here, you have a grocer's apostrophe on the home page... it's "URLs", not "URL's".
tedunangst: Depends on your style guide. Sometimes the apostrophe is preferred for abbreviations ... not something I'd correct somebody for unless we had specifically and previously agreed to a particular style guide
tedunangst claimed that was a style choice. It's not. By all these guides, "URL's" is wrong, and is something that would be corrected by editors using your examples of NYT or Chicago Manual of Style.
Also, for the periods, omitting the periods is often the cleanest answer. Instead of "C.P.A.'s" which is both ambiguous and ugly, consider "I went to my CPA's office. Naturally, it was full of CPAs."
You're safest following this line from your Wikipedia link: The MLA is explicit "do not use an apostrophe to form the plural of an abbreviation". The APA is specific in "without an apostrophe".