Here is a concrete way to construct examples of maximal commuting monoids of different cardinalities: As Anthony Quas said: we can get a maximal monoid of cardinality $|X|$
This can be generalized in the following way: let $G$ be an abelian group. Let $X$ be the $G$-set $G\sqcup Y$ where the action of $G$ on $Y$ is trivial.
Let now $f\in End(X)$ be an element which commutes with the action of $G$. We have two options:
$f(G)=G$. In this case $f$ can be thought of as an element in $G\times End(Y)$.
$f(G)=y\in Y$. In this case, $f$ can be thought of as an element of $Y\times End(Y)$ (this is just a set, not a monoid).
Take now a maximal commutative monoid $M\subseteq End(Y)$. Then we get an embedding of $G\times M$ into $End(X)$. The only way that this commutative submonoid will not be maximal is if there exists an $f\in End(X)$ from the second form. In this case $f(G)=y$ should be a fixed point of $M$, and the action of $f$ on $Y$ is given by an element in $M$.
Thus, we see that the commutative monoid $G\times M$ is almost maximal, at least in the sense that a maximal commutative monoid which contains it will have cardinality at most $|G||M|+|Y||M|$.
If $|Y|\leq |G|$, then this maximal commutative monoid will have cardinality $|G||M|$.
This enables us to construct now submonoids of many different cardinalities:
For example, if $Y$ has infinite cardinality, then we can write a bijection $Y\cong Y\times\{0,1\}$. On this set we can consider the commutative monoid $\{Id, \tau\}^Y$ where $\tau$ is the transposition. This has cardinality $2^{|Y|}$, and therefore the maximal commutative submonoid of $End(Y)$ which contains it will also be of the same cardinality. This shows that for every $|Y|\leq |X|$ we can construct a maximal commutative submonoid of cardinality max$\{|X|,2^{|Y|}\}$.
I do not know if it is possible to construct a maximal commutative monoid of cardinality smaller than $|X|$.