Variation of $\mathcal{L}_{\text{CS}}$ leads to
$$\delta \mathcal{L}_{\text{CS}}= \frac{\kappa}{2} \epsilon^{\mu \nu \rho} \partial_{\mu}\lambda \partial_{\nu} A_{\rho} - \partial_\mu \lambda J^{\mu}. \tag{1}$$
We can express this as
$$\delta \mathcal{L}_{\text{CS}}=\frac{\kappa}{2} \partial_\mu \left( \lambda \epsilon^{\mu \nu \rho} \partial_\nu A_{\rho}\right) + \lambda \partial_\mu J^{\mu},$$
by integrating by parts in the action and noticing that $\epsilon^{\mu \nu \rho} \partial_\mu \partial_{\nu} A_{\rho}=0$. Using $\partial_\mu J^{\mu}$=0, the result follows.
EDIT:
\begin{align}
\mathcal{L}'_{\text{CS}} &= \frac{\kappa}{2} \epsilon^{\mu \nu \rho} A_{\mu}' \partial_{\nu} A_{\rho}' - A_{\mu}' J^{\mu}\\
&= \frac{\kappa}{2} \epsilon^{\mu \nu \rho}(A_{\mu} + \partial_{\mu}\lambda) \partial_\nu (A_{\rho}+\partial_{\rho} \lambda) - (A_{\mu} + \partial_{\mu} \lambda) J^{\mu}\\
&=\frac{\kappa}{2}\epsilon^{\mu \nu \rho} A_{\mu} \partial_{\nu} A_{\rho} - A_{\mu} J^{\mu}+\frac{\kappa}{2}\epsilon^{\mu \nu \rho}A_{\mu} \partial_\nu \partial_{\rho} \lambda+\frac{\kappa}{2} \epsilon^{\mu \nu \rho} \partial_{\mu}\lambda \partial_{\nu} A_{\rho} - (\partial_\mu \lambda) J^{\mu}\\
&= \mathcal{L}_{\text{CS}} +\frac{\kappa}{2}\epsilon^{\mu \nu \rho}A_{\mu} \partial_\nu \partial_{\rho} \lambda+\frac{\kappa}{2} \epsilon^{\mu \nu \rho} \partial_{\mu}\lambda \partial_{\nu} A_{\rho} - (\partial_\mu \lambda) J^{\mu}.
\end{align}
Therefore the variation is
$$\delta \mathcal{L}_{\text{CS}}=\frac{\kappa}{2}\epsilon^{\mu \nu \rho}A_{\mu} \partial_\nu \partial_{\rho} \lambda+\frac{\kappa}{2} \epsilon^{\mu \nu \rho} \partial_{\mu}\lambda \partial_{\nu} A_{\rho} - (\partial_\mu \lambda) J^{\mu},$$
where the first term vanishes, since $\epsilon^{\mu \nu \rho} \partial_\nu \partial_\rho \lambda=0$.
Let's try to arrive at the same result using your approach.
$$\delta \mathcal{L}_{\text{CS}}=\frac{\partial \mathcal{L}}{\partial A_{\alpha}} \delta A_{\alpha}+ \frac {\partial \mathcal{L}}{\partial (\partial_{\beta} A_{\alpha})} \delta (\partial_{\beta} A_{\alpha}).$$
Here the two variations are
\begin{align}
\delta (\partial_{\beta} A_{\alpha}) =\partial_{\beta} \partial_\alpha \lambda \text{ and } \delta A_{\alpha} = \partial_{\alpha} \lambda
\end{align}
Using the above expressions, we can compute the individual terms of the variation.
$$\frac{\partial \mathcal{L}}{\partial A_{\alpha}} \delta A_{\alpha}=\frac{\kappa}{2} \epsilon^{\alpha \nu \rho} (\partial_{\alpha} \lambda) \partial_\nu A_{\rho} + J^{\alpha}\partial_{\alpha} \lambda \\\
\frac {\partial \mathcal{L}}{\partial (\partial_{\beta} A_{\alpha})} \delta (\partial_{\beta} A_{\alpha})=0,$$
since, again, $\epsilon^{\mu \nu \rho} \partial_\nu \partial_\rho \lambda=0$. Finally, we arrive at (1) again
$$\delta \mathcal{L}_{\text{CS}}=\frac{\kappa}{2} \epsilon^{\mu \nu \rho} \partial_{\mu}\lambda \partial_{\nu} A_{\rho} - (\partial_\mu \lambda) J^{\mu}.$$