No.
Indeed, F. Galvin proved in 1995 that every countable subset of $S_\omega$ is contained in a finitely generated subgroup (and also $S_\kappa$ for every infinite $\kappa$). By contradiction suppose $M$ exists. Let $I$ be an infinite countable subset of $M$, so $I\subset \langle F\rangle$ for some finite $F$, and hence there exists a finite subset $J$ of $M$ such that $F\subset \langle J\rangle$. Hence, for $g\in I\smallsetminus J$, we have $g\in\langle J\rangle$, and therefore $M\smallsetminus\{g\}$ generates $S_\omega$.
More generally no such $M$ exists in any uncountable group $G$ with uncountable cofinality. Indeed fix $I\subset M$, write finite subsets $I_0\subset I_1\subset I_2...$ with union $I$, and define $M_n=(M\smallsetminus I)\cup I_n$. Then $G =\bigcup\langle M_n\rangle$ (increasing union). By definition of uncountable cofinality, $G=\langle M_n\rangle$ for some $n$: contradiction. Thus this shows that for every generating subset $M$, there exists $M'\subset M$ with $M\smallsetminus M'$ infinite, such that $M'$ generates $G$.
This also shows some stronger consequence: $G$ is not "infinitely independently generated": there is no sequence $(S_n)_{n\in\omega}$ of subsets of $G$ such that $\bigcup_k S_k$ generates $G$, but $\big\langle\bigcup_{k\neq n}S_k\big\rangle\neq G$ for every $n$. The latter condition has the advantage of being purely intrinsic to the poset of subgroups of $G$.