So I need a counter example to show that $E[X|Y] = E[X]$ does not necessarily imply independence. My thought:
If $X~\sim\mathcal U(-1,1)$ and $Y=-X$, then $E[X|Y] = \int_\Omega X(\omega)P^{X|Y}(d\omega)$, but $P^{X|Y}:= \frac{P(X\cap Y)}{P(Y)}$ and, as $X$ and $Y$ never coexist, $P(X\cap Y)=0$, giving the desired result $E[X|Y] = E[X]=0$.
Is this correct? I saw an example elsewhere (after I formulated this one) that uses $Y=X^2$. But if both these work, wouldn't this then be true for any $Y=f(X)$ that is disjoint from $X$?

Your example does not work. $E[X|-X]$ is $X$ itself since $X$ is already meaurable w.r.t. $\sigma (-X)\equiv \sigma (X)$.