This is really just a long comment and figure. It summarizes the comments above and addresses the theme of the question for a natural class of knots.
In their book "Knots,'' Burde and Zieschang define a knot as an embedded subset of $S^3$ homeomorphic to $S^1$.
A general notion of equivalence for two knots $K_1,K_2$ is if they are equivalent under ambient isotopy, i.e. there is a isotopy I:$S^3 \times [0,1] \rightarrow S^3$, $I(y,t)=h_t(y)$ with $h_t$ a homeomorphism for all $t$ and
$I(x,0)=x$ and $h_1(K_1)=K_2$.
A further common restriction is that a knot is tame, i.e. the knot is equivalent to a finite sided embedded polygon in $S^3$.
A famous (and non-trivial) theorem of Gordon and Luecke states: Two tame knots are equivalent if and only if their complements are homeomorphic.
Edit: As pointed out in the comments, Gordon and Luecke's notion of equivalence is that two knots $K_1$ and $K_2$ are equivalent if and only if $K_1$ or its mirror image is ambient isotopic to $K_2$.
As pointed out in the comments, for your definitions, a knot complement is not well defined (see also "Knots" figure 1.1). Consider the trefoil knot embedded in the standard way as in the figure on right. The notice we can put a ball around the part of the knot that looks like the figure on the left and contract that ball to a point via a homotopy of $S^3$ that is also an isotopy of the knot but not the ambient space. If one used this notion of equivalence, the trefoil is equivalent to the unknot. However, by a whole host of knot invariants (Alexander polynomial, fundamental group, tri-colorability, etc.), the trefoil is a non-trivial knot.