First, it may be better to ask which quivers have a maximal green sequence. Or ask which cluster algebras have a initial seed with a maximal green sequence. Greg Muller shows in The existence of a maximal green sequence is not invariant under quiver mutation that the existence of a maximal green sequence is a property of the quiver not the cluster algebra/mutation class of quiver. In this paper an example a two mutation equivalent quivers is given such that one quiver has a maximal green sequence while the other does not.
Second I mentioned this post to Eric Bucher and he suggested the example of quivers coming from Le diagrams/reduced plabic graphs.
In Green-to-Red Sequences for Positroids by Ford and Serhiyenko it is shown that cluster algebras arising from Le diagrams have a green-to-red sequence (a.k.a. reddening sequence). Note that the existence of a green-to-red sequence does only depend on the cluster algebra. Also it is worth noting that these cluster algebra arising from a Le diagram is thought to be the coordinate ring of the corresponding positroid variety. However, the existence of a green-to-red sequence is weaker than the existence of a maximal green sequence. The existence of a maximal green sequence in this case is still open.