The motion we are considering is as described in the figure.
The position vector at time $t$ is $\vec r(t)$, while that at time $t+dt$ is $\vec r(t+dt)$. The linear displacement vector is $\vec {dr}(t) \equiv \vec r(t+dt) - \vec r(t)$. The angular displacement is shown in the figure as $d\phi$. The linear velocity is defined simply as the rate of change of the linear displacement:
$$
\vec v \equiv \frac{\vec {dr}(t)}{dt}
$$
Now, the angular velocity $\vec \omega$ is defined in two parts:
its magnitude is given by the rate of change of angular displacement
its direction is perpendicular to that of $\vec r$ and $\vec{dr}$, as determined by the thumb-rule.
To relate the angular displacement $d\phi$ to the position and displacement vectors, we make another construction.
We have drawn a line perpendicular to $\vec r(t)$ and it makes an angle $\alpha$ with $\vec {dr}$. Note that the angle between $\vec r(t)$ and $\vec{dr}$ is $\frac{\pi}{2} - \alpha$. Let the length of this perpendicular line segment be $h$. The length $h$ is given by $h/|\vec {dr}| = \cos(\alpha) \implies h = |\vec {dr}|\cos\alpha$. The angular increment $d\phi$ should be equal to the ratio of the arc length $h$ and the radius $|\vec r(t)|$. This allows us to write $d\phi = h/|\vec r(t)| = \cos\alpha \frac{|\vec {dr}|}{|\vec r(t)|}$. The magnitude of $\vec \omega$ is therefore
$$
|\vec \omega| = \frac{d\phi}{dt} = \frac{\cos\alpha}{|\vec r(t)|} \frac{|\vec {dr}|}{dt}
$$
The direction of $\vec \omega$ is given by the thumb rule, and it is expressed by the cross-product:
$$\hat \omega = \frac{\vec r(t)\times \vec{dr}}{|\vec r(t)\times \vec{dr}|} = \frac{\vec r(t)\times \vec{dr}}{|\vec r(t)||\vec{dr}|\cos\alpha}$$
Note that the denominator has $\cos\alpha$ instead of $\sin\alpha$ because the angle between $\vec r(t)$ and $\vec{dr}$ is $\pi/2-\alpha$.
Combining the direction and the magnitude, we get
$$\vec \omega = \frac{\vec r(t)\times \vec{dr}}{|\vec r(t)|^2 dt}$$
Using the vector triple product formula, we get
$$\vec \omega \times \vec r = \frac{|\vec r(t)|^2 \vec{dr} - (\vec r(t)\cdot \vec{dr})\vec r(t)}{|\vec r(t)|^2 dt} = \vec v - (\hat r(t)\cdot \vec v)\hat r(t)$$
For circular motion, the linear velocity is always perpendicular to the position vector, so the second term vanishes. In that special case, we can conclude that
$$\vec \omega \times \vec r = \vec v$$