Punctuation after multiline math diagram

I suggest you put it in the diagram but hide its width so B is not horizontally shifted in relation to the arrow. Also you should center the diagram with respect to the equation number:

\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{amsmath}

\usepackage[all]{xy}

\begin{document}

\begin{equation}
  \vcenter{\xymatrix{
  A\ar[d]\\
  B\rlap{\ .}
  }}
\end{equation}

\end{document}

I would judge how much space to put before the dot according to the surrounding text. Nothing or \, might be better than what I have given.