I assume that the morphisms on the von Neumann algebra side are unital *-homomorphisms.

For a group morphism $\theta:G\rightarrow H$, the algebraic morphism (on the twisted group algebra, over the ring of finitely supported functions on $G$) is given by $\psi_{alg}(\delta_g u_h)=\delta_{\theta(g)}u_{\theta(h)}$ where $\delta_g\in L^\infty(G)$ is the characteristic function of the singleton $\{g\}$. First of all, observe that $\theta$ has to be injective in order to make $\psi_{alg}$ multiplicative. If this algebraic morphism is to extend to a unital morphism of the crossed product, it follows that $\psi(1)=\sup\{\psi(\delta_g)\mid g\in G\}=\sup\{\delta_{\theta(g)}\mid g\in G\}$ and hence $\theta$ is surjective.

So we have shown that both constructions (a) and (b) are functorial with respect to isomorphisms, but not with respect to any other morphisms.

However, in case (a) we can give a pathological functorial structure. We restrict the objects to countably infinite groups, and assume that they come with a bijection $n:N\rightarrow G$. Observe that the group-measure space construction gives $B(\ell^2(G))$ which is now canonically isomorphic to $B(\ell^2(N))$, say by the isomorphism $\psi_G$. Mapping all morphisms $\theta:G\rightarrow H$ to the isomorphism $\psi_\theta=\psi_H^{-1}\circ\psi_G$ gives us a pathologial functor.

I do not know if (b) also has such a pathological functor, but it is in any case not the one we are interested in.