There are infinitely many positive integers $n$ such that $S_n$ has an abelian subgroup of order $n^2-1$.
Suppose $n$ is odd. Let $u\in\{-1,+1\}$ be such that $n\equiv u\pmod{4}$. Then, $$n^2-1=2^{k+1}\,\left(\frac{n-u}{2^k}\right)\,\left(\frac{n+u}{2}\right)\,,$$
where $2^k$ is the largest power of $2$ that divides $n-u$ (whence $k\geq 2$). If
$$2^{k+1}+\left(\frac{n-u}{2^k}\right)+\left(\frac{n+u}{2}\right)\leq n\,,$$
then there exists an abelian subgroup of $S_n$ of order $n^2-1$, which is the product of three cyclic groups generated by cycles of length $2^{k+1}$, $\frac{n-u}{2^k}$, and $\frac{n+u}{2}$. Note that the inequality above is equivalent to
$$n-u\geq\frac{2^{k+2}}{1-\frac{1}{2^{k-1}}}\,.$$
Hence, if $n-u=2^kq$, where $q\geq 9$ is an odd integer, then $S_n$ has a subgroup of order $n^2-1$. In other words, if $$n=2^k(2r+1)\pm1$$ where $k\geq 2$ and $r\geq 4$ are integers, then $S_n$ has a subgroup of order $n^2-1$.
P.S. I made a stupid calculation error in my earlier answer (now deleted).