We need a Lorentz transformation which will make $\vec{E}$ and $\vec{B}$ from inertial frame $S$ parallel in an inertial frame $S'$, i.e. $\vec{E'} \times \vec{B'} = 0$. Consider $c=1$ for calculations.
Let us try $\vec{v'} = \alpha (\vec{E} \times \vec{B})$ for some $\alpha \in \mathbb{R}/\{0\}$. Here, $v'$ denotes the velocity of the frame $S'$ with respect to $S$.
Then, $$\vec{E'} = \gamma(\vec{E}+\vec{v'}\times\vec{B}) = (1 - \alpha B^2) \vec{E}+\alpha (\vec{E} \cdot \vec{B}) \vec{B} \\
\vec{B'} = \gamma(\vec{B}-\vec{v'}\times\vec{E}) = (1 - \alpha E^2) \vec{B}+\alpha (\vec{E} \cdot \vec{B}) \vec{E}$$
Case 1 (a): Of course, as you mentioned, if $\vec{E} \cdot \vec{B} = 0$ and $|\vec{E}|=|\vec{B}|=0$, $\vec{E'}$ and $\vec{B'}$ cannot be made parallel.
Case 1 (b): Even if $\vec{E} \cdot \vec{B} = 0$, but $E^2 \ne B^2$, we can make either $\vec{E'}$ or $\vec{B'}$ zero, by choosing $\alpha = \displaystyle\frac{1}{\text{max}(E^2, B^2)}$
Case 2: Suppose, $\vec{E} \cdot \vec{B} \ne 0$, then $\vec{E'}$ and $\vec{B'}$ can be made parallel by choosing an $\alpha$ such that $$\alpha^2 [(\vec{E} \cdot \vec{B})^2 - E^2B^2] = 1 - \alpha(E^2+B^2).$$ The relative velocity $\vec{v'}$ of the frame $S'$ with respect to the inertial frame $S$ is given by
$$\frac{\vec{v'}}{1+ v'^2} = \frac{\alpha(\vec{E}\times\vec{B})}{1+\alpha^2({\vec{E}\times \vec{B}})^2} = \frac{\alpha (\vec{E}\times \vec{B})}{1+\alpha^2[E^2B^2-(\vec{E} \cdot \vec{B})^2]}= \frac{\vec{E}\times\vec{B}}{E^2+B^2}.$$