We show the problem of counting homomorphisms from the fundamental group of a homology 3-sphere M to a finite, non-abelian simple group G is #P-complete, in the case that G is fixed and M is the computational input. Similarly, deciding if there is a non-trivial homomorphism is NP-complete. In both reductions, we can guarantee that every non-trivial homomorphism is a surjection. As a corollary, for any fixed integer m ≥ 5, it is NP-complete to decide whether M admits a connected m-sheeted covering.Our construction is inspired by universality results in topological quantum computation. Given a classical reversible circuit C, we construct M so that evaluations of C with certain initialization and finalization conditions correspond to homomorphisms π 1 (M) → G. An intermediate state of C likewise corresponds to a homomorphism π 1 (Σ g ) → G, where Σ g is a pointed Heegaard surface of M of genus g. We analyze the action on these homomorphisms by the pointed mapping class group MCG * (Σ g ) and its Torelli subgroup Tor * (Σ g ). By results of Dunfield-Thurston, the action of MCG * (Σ g ) is as large as possible when g is sufficiently large; we can pass to the Torelli group using the congruence subgroup property of Sp(2g, Z). Our results can be interpreted as a sharp classical universality property of an associated combinatorial (2 + 1)-dimensional TQFT.