You can do this by thinking carefully about the orbits of points under the various group actions. I'll look at the case where $q'q\equiv 1 \bmod p$ first.
Under the action of $\mathbb{Z}/p\mathbb{Z}$, given by $(z_1,z_2)\mapsto (z_1e^{2\pi i / p},z_2 e^{2\pi i q / p})$ the orbit of the point $(w_1,w_2)$ is the set
$$O_1=\{(w_1e^{2\pi i k / p},w_2 e^{2\pi i kq / p})\,|\, k=0, \dots, p-1\}.$$
Now we study orbit of $(w_2,w_1)$, the under the action given by
$(z_1,z_2)\mapsto (z_1e^{2\pi i / p},z_2 e^{2\pi i q' / p})$. This orbit is
$$O_2=\{(w_2e^{2\pi i k' / p},w_1 e^{2\pi i k'q' / p})\,|\, k'=0, \dots, p-1\},$$
which, by substituting $k'=kq \bmod p$, can be rewritten as
$$O_2=\{(w_2e^{2\pi i kq / p},w_1 e^{2\pi i k / p})\,|\, k=0, \dots, p-1\}.$$
Thus the map $\phi \colon S^3 \rightarrow S^3$ given by
$\phi(z_1,z_2)=(z_2,z_1)$ carries the orbit $O_1$ of $(w_1,w_2)$ under the first action onto the orbit $O_2$ of $(w_2,w_1)$ under the second action, thus inducing a diffeomorphism between $L(p,q)$ and $L(p,q')$ where $qq'\equiv 1 \bmod p$.
The case of $-q$ is similar. Consider the orbit of $(w_1,\overline{w_2})$, the under the action given by
$(z_1,z_2)\mapsto (z_1e^{2\pi i / p},z_2 e^{-2\pi i q / p})$. This orbit is
$$O_3=\{(w_1 e^{2\pi i k' / p}, \overline{w_2} e^{-2\pi i k'q / p})\,|\, k'=0, \dots, p-1\}.$$
Thus $O_3$ is the image of $O_1$ under the map $\psi\colon S^3\rightarrow S^3$ given by $\psi(z_1,z_2)=(z_1,\overline{z_2})$. Thus $\psi$ induces a diffeomorphism between $L(p,q)$ and $L(p,-q)$. Here I'm using $\overline{z}$ to denote complex conjugation.