Regarding the original question: I think that ultimately the sense in which functor calculus is like stacks is that we are peforming localizations of a functor category. Moreover, these localizations are left exact. This leads to similarities in how the localizations are described (via descent with respect to certain "covering" diagrams, which can be described as (hyper)covers if you like) and how the localizations are constructed. More on this below.
Regarding the analogy between manifold calculus and Goodwillie calculus: In both cases, we have a tower of localizations of a functor category $Fun(C,D)$. In both cases, we have natural descriptions of the localizations in terms of descent with respect to certain "covering" diagrams, and in both cases the tower of localizations corresponds to a filtration of the collection of "covering" diagrams for the strongest localization.
But I don't think these filtrations arise in analogous ways. In the manifold calculus, the strongest localization comes from the usual Grothendieck topology on the site of manifolds: "covers" are Cech covers in the usual sense; the $n$th localization is at the subcollection of $n$-Weiss covers as described by Dmitri Pavlov. In the homotopy calculus, we start with a "cover" being any strongly cartesian cube in $Spaces^{op}$; the $n$th localization is obtained by restricting to cubes of dimension $\geq n+1$. There's no Weiss anything in sight.
But I don't think these filtrations arise in analogous ways. In the manifold calculus, the strongest localization comes from the usual Grothendieck topology on the site of manifolds: "covers" are Cech covers in the usual sense; the $n$th localization is at the subcollection of $n$-Weiss covers as described by Dmitri Pavlov. In the homotopy calculus, we start with a "cover" being any strongly cartesian cube in $Spaces^{op}$; the $n$th localization is obtained by restricting to cubes of dimension $\geq n+1$. There's no Weiss anything in sight.