The prime factorization of 21 (7x3) seems to be the largest done to date with Shor's algorithm; it was done in 2012 as detailed in this paper. It should be noted, however, that much larger numbers, such as 56,153 in 2014, have been factored using a minimization algorithm, as detailed here. For a convenient reference, see Table 5 of this paper:
$$
\begin{array}{c}
\textbf{Table 5:}~\text{Quantum factorization records} \\ \hline
\small{
\begin{array}{cccccc}
\text{Number} & \text{# of factors} & \begin{array}{c}\text{# of qubits} \\ \text{needed} \end{array} & \text{Algorithm} & \begin{array}{c}\text{Year} \\ \text{implemented} \end{array} & \begin{array}{c}\text{Implemented} \\ \text{without prior} \\ \text{knowledge of} \\ \text{solution} \end{array} \\ \hline
15 & 2 & 8 & \text{Shor} & 2001~\left[2\right] & \chi \\
& 2 & 8 & \text{Shor} & 2007~\left[3\right] & \chi \\
& 2 & 8 & \text{Shor} & 2007~\left[3\right] & \chi \\
& 2 & 8 & \text{Shor} & 2009~\left[5\right] & \chi \\
& 2 & 8 & \text{Shor} & 2012~\left[6\right] & \chi \\
21 & 2 & 10 & \text{Shor} & 2012~\left[7\right] & \chi \\
143 & 2 & 4 & \text{minimization} & 2012~\left[1\right] & \checkmark \\
56153 & 2 & 4 & \text{minimization} & 2012~\left[1\right] & \checkmark \\ \hline
291311 & 2 & 6 & \text{minimization} & \text{not yet} & \checkmark \\
175 & 3 & 3 & \text{minimization} & \text{not yet} & \checkmark
\end{array}}
\end{array}_{\Large{.}}
$$