You don't actually need choice for this, assuming the $A_j$'s are disjoint. Note that the proposition you want to prove is actually false in general (see Thomas' comment on your question or Paul K's comment on my answer) but it is true if you add the disjointness assumption.
Disjointness implies that we can define a function $f\colon\cup_{j \in J} A_j \to J$ without having to make any choices by sending $x$ to $j$ if $x\in A_j$, and moreover $f$ is surjective iff each $A_j$ is non-empty. Therefore if the union is countable then $J$ must be as well, since it is the image of a countable set.
You could then apply this to your manifolds problem as follows. An arbitrary disjoint union of manifolds will still be Hausdorff and locally Euclidean, so we we only need to be concerned with second countability. What I will actually show is
Suppose $X = \cup_{j\in J} X_j$ where each $X_j$ is non-empty and $X_i\cap X_j =\emptyset$ for every $i\neq j$. If $X$ has a countable basis then $J$ is countable.
Suppose $A$ is a countable basis for $X$. One property of a basis is that any open set of $X$ can be written as a union of elements of $A$. In particular, if we have an open set $U\subset X_j$ for some $j$, then $U$ will be the union of elements in $A$, which will necessarily be subspaces of $X_j$. Therefore the following is also a basis, and will still be countable since it is a subset of $A$:
$$A' = \{ U \in A\ |\ U\subset X_j\text{ for some }j\}.$$ If we let $A_j = \{ U \in A\ |\ U\subset X_j\}$, this will be a basis for $X_j$ and therefore non-empty since $X_j$ is non-empty, and $A_i \cap A_j = \emptyset$ for $i\neq j$. Then since $A' = \cup_{j\in J} A_j$ it follows from the above that $J$ must be countable.
Note that this argument didn't depend on the $X_j$'s being manifolds, the only input was second countability of $X$, and the non-empty/disjointess.