The case of $\mathbb N$ requires no axiom of choice, and we can prove it to be countable. Here is how:
Note that $\pi\colon\mathbb N\to\mathbb N$ is a permutation with a finite support if and only if there exists some $k$ such that $\pi(n)=n$ for all $n>k$. Therefore for every such $\pi$ there is some $k(\pi)$ such that $\pi$ is actually a permutation of $\{0,\ldots,k-1\}$.
Now since every for every $k$ there are only finitely many permutations of $\{0,\ldots,k-1\}$ we would like to conclude that this is a countable union of finite sets and therefore countable. Assuming the axiom of choice (or even axiom of choice for finite sets) would conclude this portion of the proof.
Without the axiom of choice, however, we still have some work a head of us.
Let us define the following sequence of sets
$$A_k = \{\pi\mid k(\pi)=k\}$$ That is all the permutations that $k$ is the maximal $k$ moved.
Note that for $m<k$ we have $A_m\subsetneq A_k$. Now we will define inductively an enumeration of $A=\bigcup_{k\in\mathbb N} A_k$.
For $k=2$ we have the first nonempty $A_k$, and it only has one element so we are done.
Suppose $A_k$ was ordered by $<_k$, we define the order $<_{k+1}$ on $A_{k+1}$ as follows, for any $\tau,\pi\in A_k$:
$$\pi<_{k+1}\tau\iff
\begin{cases}
&\pi,\tau\in A_k&\land&\pi<_k\tau &\text{ or}\\
&\pi\in A_k&\land&\tau\notin A_k &\text{ or}\\
&\pi,\tau\notin A_k&\land&\pi(n)<\tau(n)\text{ where } n=\min\{t<k\mid \pi(t)\neq\tau(t)\}
\end{cases}$$
Let us verify that this is indeed a linear order, for any $\pi,\tau\in A_{k+1}$ either both in $A_k$, or at one of them is not in which cases it is clear that the two permutations are comparable, and if both of them in $A_{k+1}$ then there is some $n$ for which $\pi(n)\neq\tau(n)$ or else $\pi=\tau$.
It is also clear why $<_{k+1}$ when restricted to $A_k$ is exactly $<_k$. Lastly since every finite linear order is a well-order this gives us an increasing chain of linear orders on increasing subsets of $A$.
Let $\prec=\bigcup_k <_k$, then $\prec$ is a well ordering of $A$, and it is countable as it is the limit of finite well-orderings. Therefore $A$ has a countable enumeration by $\prec$. $\square$
A note on the general case without the axiom of choice:
While assuming the axiom of choice we may replace $\mathbb N$ at the above proof by any other set, and the proof will only change by a little bit. We could in fact generalize it without much trouble either to include even larger support for larger sets.
However, in the absence of choice things are not that pretty. Without the axiom of choice we have a may have an infinite set $S$ such that $f\colon S\to S$ is bijective then it has a finite support. However the set of all permutations of $S$ will have a strictly larger cardinality than that of $S$.
Assuming, though, that $S$ can be well-ordered then things are fine again, and the above proof works (changing the necessary details for it to fit $|S|$).