Varioref, cleveref and autonum together

Since it seems you want the \vref command to work with Comma Separated Lists, you should use \autonum@generatePatchedReferenceCSL{vref} as in the following.

\documentclass{article}
\usepackage[%
  paperwidth=3in,
  paperheight=2in,
  margin=0.1in,
  bottom=0.3in,
  footskip=0pt]{geometry} % Only to get smaller pages for MWE

\usepackage{amsmath}

\usepackage{varioref}
\usepackage{cleveref}

\usepackage{autonum}

\makeatletter
\autonum@generatePatchedReferenceCSL{vref}
\makeatother

\begin{document}

\begin{align} x \label{eqnx} \end{align} % referenced, must have number (1)
\begin{align} y \label{eqny} \end{align} % referenced, must have number (2)
\begin{align} z \label{eqnz} \end{align} % not referenced, must not have any number

\pagebreak

\vref{eqnx,eqny}

\end{document}

From section 3.3 "Reference commands" in the documentation:

For reference commands expecting a comma separated list of label names as an argument, you can use \autonum@generatePatchedReferenceCSL{NewReferenceCommand}.