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\documentclass[12pt,letterpaper]{article}
\usepackage[T1]{fontenc}
\usepackage{amsmath}
\begin{document}
\noindent
Is this the proper way of placing the footnote number\footnote{A footnote.} :
\begin{equation}
y(x) = x^2,
\end{equation}
Or is this the proper way of placing the footnote number :\footnote{A footnote.}
\begin{equation}
y(x) = x^2,
\end{equation}
\end{document}