First observe that $M$ cannot be a closed manifold[Alexander Duality is an obstruction for that]. Also observe that $M$ is orientable.[the same duality works again] Now claim is that all it's boundary components are sphere. Observe that $rk(H_1(M,\mathbb Z))\geq rk(H_1(\partial M)/2$ [ basically half of the boundary homology dies]. So $H_1=0$ forces that $H_1(\partial M)=0$. By classification of surfaces, it can only be $S^2$ (since it has a induced orientation from $M$]. Now use higher dimension Jordan separation theorem. Since $M$ is in $\mathbb R^3$, all the boundary sphere should lie inside one of the componenet, called it as outer most component. Since as we observe that $M$ is orientable and compact, so either $M$ is $D^3$ or $D^3-$balls removed. In both the cases $\pi_1=0$. Hence complete the proof.
Observe that if $M$ is non-compact, then it is not true. In Hatcher you can see that unbounded open region of the complement of Alaxander horned sphere is a counter example.