You don't need any algebraic topology for that!
Of course it is not true in general, since you can always cover $Y$ by $Y\times F$, where $F$ is an uncountable discrete space. But you have strong assumptions that exclude such pathology.
I'm also posting this answer to provide some details (in the last paragraph) that I find important and that were skipped in the brief explanation provided by Jim.
For each $p\in Y$ take an evenly covered neighbourhood. Since we work with a manifold, fix a smaller neighbourhood $B(p)$ diffeo with a unit ball in $\mathbb R^n$ and a family of its subneighbourhoods diffeo with balls forming a local basis at $p$. Now, take a basis $\mathcal B'$ of $X$ consisting of all those balls. By this question and the assumption that there is some countable basis $\mathcal V$ for $X$ you can choose a countable subbasis of $\mathcal B'$ - let's call it $\mathcal B$.
Now - for each $B\in \mathcal B$ we have $f^{-1}(B)\simeq B\times F_{B}$ for some discrete space $F_{B}$. Note that $F_{B}$ is at most countable because components of $B\times F_{B}$ are exactly of the form $B\times \{g\}$, where $g\in F_{B}$.
Our basis of $Y$ will be
$$\tau=\bigcup_{B\in \mathcal B} \left\{B\times \{g\}\ | \ g\in F_{B} \right\}.$$
It is clearly countable as a countable union of at most countable sets.
Why is it a basis? We know that $f$ is a local homeomorphism, so it preserves local bases. Did we utilise it well?
That's where our balls (coming from the assumption that we deal with a manifold, not a random second countable space!) are used. Having $p\in B_0\in \mathcal B$ and a sheet $B_0 \times \{g\}$ of its inverse image, we know that the local basis $\mathcal B_p^{B_0}$ at $p$ (restricted to subsets of $B_0$) is "transported" to $B_0 \times \{g\}$ (by that I mean that one of the sheets [that form $\tau$] over any set from $\mathcal B_p^{B_0}$ must lie inside $B_0 \times \{g\}$, because the representation as a product with a discrete space is the same for the subset). It doesn't have to be true in the case of not connected neighbourhoods!