This is slightly indirect way of approaching the problem but just for sake of variety I am adding a new approach.
Making the substitution $k \mapsto n-j$,
$$\sum_{k=0}^{n} (-1)^{n-k}\binom{n+k}{n-k}x^{2k} = \sum_{j = 0}^{n} (-1)^{j}\binom{2n-j}{j}x^{2n-2j} = U_{2n}\left(\frac{x}{2}\right)$$
where, $U_{n}(x)$ is the Chebyshev Polynomial of the second kind. See here for an elementary proof of the rightmost equality.
Making the substitution $x = 2\cos \theta$, we may write the above expresion as:
$$U_{2n}\left(\frac{2\cos \theta}{2}\right) = \frac{\sin (2n+1)\theta}{\sin \theta}$$
Thus, $$\begin{align}\sum_{k=0}^{n} \frac{(-1)^{n-k}}{2k+1}\binom{n+k}{n-k} &= \int_0^1 \sum_{k=0}^{n} (-1)^{n-k}\binom{n+k}{n-k}x^{2k} \,\mathrm{d}x \\
&= \int_0^1 U_{2n}(x/2)\,\mathrm{d}x\\&= 2\int_{\pi/3}^{\pi/2} \sin (2n+1)\theta \,\mathrm{d}\theta \\
&= \left.-2\frac{\cos (2n+1)\theta}{2n+1}\right\vert_{\pi/3}^{\pi/2}\\
&= \frac{2}{2n+1}\cos \left(\frac{(2n+1)\pi}{3}\right)\end{align}$$
as required.