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As Ryan says, this follows from Waldhausen's paper, when appropriately interpreted. Sufficiently large 3-manifolds are usually called "Haken" in the literature, and as Ryan says, they are irreducible and contain an incompressible surface (which means that the surface is incompressible and boundary incompressible). An irreducible manifold with non-empty boundary and not a ball (ie no 2-sphere boundary components) is always sufficiently large, by a homology and surgery argument. By the sphere theoremAlexander's Lemma, knot complements are irreducible, and therefore sufficiently large (the sphere theorem implies that they are aspherical).

Waldhausen's theorem implies that if one has two sufficiently large 3-manifolds $M_1, M_2$ with connected boundary components, and an isomorphism $\pi_1(M_1) \to \pi_1(M_2)$ inducing an isomorphism $\pi_1(\partial M_1) \to \pi_1(\partial M_2)$, then $M_1$ is homeomorphic to $M_2$. This is proven by first showing that there is a homotopy equivalence $M_1\simeq M_2$ which restricts to a homotopy equivalence $\partial M_1\simeq \partial M_2$. Then Waldhausen shows that this relative homotopy equivalence is homotopic to a homeomorphism by induction on a hierarchy. The peripheral data is necessary if the manifold has essential annuli, for example the square and granny knots have homotopy equivalent complements.

If $K_1, K_2\subset S^3$ are (tame) knots, and $M_1=S^3-\mathcal{N}(K_1), M_2=S^3-\mathcal{N}(K_2)$ are two knot complements, then Waldhausen's theorem applies. However, one must also cite the knot complement problem solved by Gordon and Luecke, in order to conclude that $K_1$ and $K_2$ are isotopic knots. Otherwise, one must also hypothesize that the isomorphism $\partial M_1 \to \partial M_2$ takes the meridian to the meridian (the longitudes are determined homologically). This extra data is necessary to solve the isotopy problem for knots in a general 3-manifold $M$, to guarantee that the homeomorphism $(M_1,\partial M_1)\to (M_2,\partial M_2)$ extends to a homeomorphism $(M,K_1)\to (M,K_2)$, since for example there are knots in lens spaces which have homeomorphic complements by a result of Bleiler-Hodgson-Weeks.

2 added 134 characters in body

As Ryan says, this follows from Waldhausen's paper, when appropriately interpreted. Sufficiently large 3-manifolds are usually called "Haken" in the literature, and as Ryan says, they are irreducible and contain an incompressible surface (which means that the surface is incompressible and boundary incompressible). An irreducible manifold with non-empty boundary and not a ball (ie no 2-sphere boundary components) is always sufficiently large, by a homology and surgery argument. By the sphere theorem, knot complements are irreducible, and therefore sufficiently large.

Waldhausen's theorem implies that if one has two sufficiently large 3-manifolds $M_1, M_2$ with connected boundary components, and an isomorphism $\pi_1(M_1) \to \pi_1(M_2)$ inducing an isomorphism $\pi_1(\partial M_1) \to \pi_1(\partial M_2)$, then $M_1$ is homeomorphic to $M_2$. This is proven by first showing that there is a homotopy equivalence $M_1\simeq M_2$ which restricts to a homotopy equivalence $\partial M_1\simeq \partial M_2$. Then Waldhausen shows that this relative homotopy equivalence is homotopic to a homeomorphism by induction on a hierarchy. The peripheral data is necessary if the manifold has essential annuli, for example the square and granny knots have homotopy equivalent complements.

If $K_1, K_2\subset S^3$ are (tame) knots, and $M_1=S^3-\mathcal{N}(K_1), M_2=S^3-\mathcal{N}(K_2)$ are two knot complements, then Waldhausen's theorem applies. However, one must also cite the knot complement problem solved by Gordon and Luecke, in order to conclude that $K_1$ and $K_2$ are isotopic knots. Otherwise, one must also hypothesize that the isomorphism $\partial M_1 \to \partial M_2$ takes the meridian to the meridian (the longitudes are determined homologically). This extra data is necessary to solve the isotopy problem for knots in a general 3-manifolds, 3-manifold $M$, to guarantee that the homeomorphism $(M_1,\partial M_1)\to (M_2,\partial M_2)$ extends to a homeomorphism $(M,K_1)\to (M,K_2)$, since for example there are knots in lens spaces which have homemorphic homeomorphic complements by a result of Bleiler-Hodgson-Weeks.

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As Ryan says, this follows from Waldhausen's paper, when appropriately interpreted. Sufficiently large 3-manifolds are usually called "Haken" in the literature, and as Ryan says, they are irreducible and contain an incompressible surface (which means that the surface is incompressible and boundary incompressible). An irreducible manifold with non-empty boundary and not a ball (ie no 2-sphere boundary components) is always sufficiently large, by a homology and surgery argument. By the sphere theorem, knot complements are irreducible, and therefore sufficiently large.

Waldhausen's theorem implies that if one has two sufficiently large 3-manifolds $M_1, M_2$ with connected boundary components, and an isomorphism $\pi_1(M_1) \to \pi_1(M_2)$ inducing an isomorphism $\pi_1(\partial M_1) \to \pi_1(\partial M_2)$, then $M_1$ is homeomorphic to $M_2$. This is proven by first showing that there is a homotopy equivalence $M_1\simeq M_2$ which restricts to a homotopy equivalence $\partial M_1\simeq \partial M_2$. Then Waldhausen shows that this relative homotopy equivalence is homotopic to a homeomorphism by induction on a hierarchy. The peripheral data is necessary if the manifold has essential annuli, for example the square and granny knots have homotopy equivalent complements.

If $K_1, K_2\subset S^3$ are (tame) knots, and $M_1=S^3-\mathcal{N}(K_1), M_2=S^3-\mathcal{N}(K_2)$ are two knot complements, then Waldhausen's theorem applies. However, one must also cite the knot complement problem solved by Gordon and Luecke, in order to conclude that $K_1$ and $K_2$ are isotopic knots. Otherwise, one must also hypothesize that the isomorphism $\partial M_1 \to \partial M_2$ takes the meridian to the meridian (the longitudes are determined homologically). This extra data is necessary to solve the isotopy problem for knots in general 3-manifolds, since for example there are knots in lens spaces which have homemorphic complements by a result of Bleiler-Hodgson-Weeks.