The point is that by your construction $f:\mathcal{E}_\Gamma\to Y_\Gamma$ is an elliptic surface with a *section* $\sigma$. So as Keerthi said in the comments, $f$ is projective. In fact the relative divisor $3\sigma$ gives the Weirstrass embedding $\mathcal{E}_\Gamma\to \mathbb{P}(f_*\mathcal{O}(\sigma))$).
(Ben's comment shows that projectivity can fail without a section.) 
From here, quasiprojectivity is
straight forward: If $V$ is an extension of 
$f_*\mathcal{O}(\sigma))$ to the smooth projective closure  $ Y_\Gamma$, then
the closure of $\mathcal{E}_\Gamma$ in $\mathbb{P}(V)$ is projective.