How to align numbers in parentheses

Here are two ways: either use a \phantom{-} for the number without a – (to be used for each such number), or load mathtools and use its pmatrix* environment, which allows for an optional alignment specifier:

\begin{equation*}
    x = \begin{pmatrix*}[r] 
            4 \\
           -3 \\
        \end{pmatrix*}
        \qquad
    x = \begin{pmatrix}
        \phantom{-} 4 \\
           -3 \\
        \end{pmatrix}
 \end{equation*}

\documentclass{article}

\usepackage{amsmath}

\begin{document}

\[
\left(  \begin{array}{@{}r@{}}
    4\\-3
  \end{array}\right)
\]
\end{document}

\documentclass[12pt]{article}
\usepackage{stackengine}
\setstackEOL{\\}
\begin{document}
\[
x=\parenVectorstack[r]{4\\-3}
\]
\end{document}