The key to answering this question is the clutching construction. Let $p_1, p_2$ be antipodal points on $S^2$ and define $U_i = S^2\setminus\{p_i\}$. Note that $U_i$ is homeomorphic to $\mathbb{R}^2$ (via stereographic projection) and therefore contractible.
Suppose $E$ is an $S^1$-bundle over $S^2$, then as $U_1$, $U_2$ are contractible, $E|_{U_1}$ and $E|_{U_2}$ are trivial; i.e. there are bundle isomorphisms $\psi_i : E|_{U_i} \to U_i\times S^1$. Therefore, the bundle $E$ is completely determined by the transition map $\phi_{12} : U_1\cap U_2 \to \operatorname{Homeo}(S^1)$ which satisfies
$$\psi_2|_{U_1\cap U_2} = (\operatorname{id}_{U_1\cap U_2}, \phi_{12})\circ\psi_1|_{U_1\cap U_2}.$$
It turns out that isomorphism classes of such bundles correspond to homotopy classes of such maps. That is, isomorphism classes of $S^1$-bundles over $S^2$ are in one-to-one correspondence with homotopy classes of maps $U_1\cap U_2 \to \operatorname{Homeo}(S^1)$, i.e. $[U_1\cap U_2, \operatorname{Homeo}(S^1)]$. Note that $U_1\cap U_2$ deformation retracts onto $S^1$ (the equator of $S^2$), so
$$[U_1\cap U_2, \operatorname{Homeo}(S^1)] = [S^1, \operatorname{Homeo}(S^1)] = \pi_1(\operatorname{Homeo}(S^1)).$$
In order to compute this, we use the fact that $\operatorname{Homeo}(S^1)$ deformation retracts onto $O(2)$ and therefore $\pi_1(\operatorname{Homeo}(S^1)) = \pi_1(O(2)) = \mathbb{Z}$.
I see that Mike Miller has now posted an answer, so I will stop here as his answer addresses the general picture.