I ran across this reading the introduction to Siegel's New York Practice (Fourth Edition). Apparently up until 1978 a section could be changed only by the legislature and a rule could be changed by the legislature or Judicial Conference. In 1978, the section of the Judiciary Law delineating the difference between the two was repealed and the distinction was lost. Now only the legislature can make changes (though Siegel is clear that this isn't entirely clear).
Also, as I'm sure at least two of you readers have noticed, courts rarely indicate whether they are citing a section or rule. CPLR § 101(Short title; application) allows such citation.
If you're interested, you can find all this on page 3 of the introduction in the softcover version.