For basic Mayer-Vietoris usage you need to thicken your link/knot a little in such way that you won't create new intersections in obtained in such way "link" of solid tori.
Namely: let $K$ be your link of $n$ circles and $U_1 = K \times D^2_{3 \varepsilon}$, where $D_{3 \varepsilon}^2$ is disk of "small" radius $3 \varepsilon$ such that you can retract $U_1$ to $K$. Then let's denote by $U_2 = S^3 \setminus \{K \times D^2_{ \varepsilon}\}$ it's thickened complement. MV sequence gives us:
$$\ldots\rightarrow H_2(U_1 \cup U_2) \rightarrow H_1(U_1 \cap U_2) \rightarrow H_1(U_1) \oplus H_1(U_2) \rightarrow H_1(U_1 \cup U_2) \rightarrow \ldots$$
$$\ldots\rightarrow H_2(S^3) \rightarrow H_1(U_1 \cap U_2) \rightarrow H_1(U_1) \oplus H_1(U_2) \rightarrow H_1(S^3) \rightarrow \ldots$$
$$\ldots0 \rightarrow H_1(U_1 \cap U_2) \rightarrow H_1(U_1) \oplus H_1(U_2) \rightarrow 0 \rightarrow \ldots.$$
Observe now that:
$U_1 \cap U_2$ is homologically disjoint sum of $n$ tori and hence $H_1(U_1 \cap U_2) = \bigoplus_{i=1}^n \mathbb{Z}\oplus \mathbb{Z}$
$H_1(U_1) = \bigoplus_{i=1}^n \mathbb{Z}$
$H_1(U_2) = H_1(S^3 \setminus K)$
hence $H_1(S^3 \setminus K) = \bigoplus_{i=1}^n \mathbb{Z}$.
The problem with this approach is that it depends on the embedding of $K$ in $S^3$. It may not be possible to find described small $\varepsilon$ (search for "wild knots"). However Qiaochu already mentioned the workaround - Alexander Duality which gives the result immediately.