Yes.
First, suppose for contradiction that there is no constant $M>0$ such that, for any countable $C \subset X$, there is an $x \in X\setminus C$ so that $d(x,y) > M$ for all $y \in C$. Then taking $C_n$ to be a counterexample for $M = \frac{1}{n}$, we can see that $\bigcup_n C_n$ is a countable dense set. Since $X$ is not separable this is a contradiction and there must be such an $M>0$. Fix such an $M$.
Now proceed by transfinite recursion to construct $N$. Let $N_0$ consist of a single element, and construct $N_\alpha$ for each countable ordinal $\alpha$, so that $N_\alpha$ satisfies $\forall x, y \in N_{\alpha} (d(x,y)>M)$, in the following way: at countable stages $\alpha+1$, $N_{\alpha+1} = N_\alpha \cup \{x\}$, where $x \in X\setminus N_\alpha$ is the element which must exist by the preceding paragraph. Then $N_{\alpha+1}$ has the property that $N_{\alpha+1}$ is countable and $d(x,y) > M$ for all $x, y \in N_{\alpha+1}$. At limit stages, just take unions, so that $\displaystyle N_\alpha = \bigcup_{\beta<\alpha} N_\beta$ for limit ordinals $\alpha$. It's easy to see that $N_\alpha$ has the required property in this case as well. This recursion can proceed up to $\alpha=\omega_1$, the first uncountable ordinal. Take $\displaystyle N = N_{\omega_1} = \bigcup_{\alpha<\omega_1} N_\alpha$. This is our required set $N$.