Here's an alternative proof (at least, an alternative wording), making $H$ very explicit.
For $r$ the rank, let $G\to\mathbf{Z}^r$ be a surjective homomorphism (e.g., take the abelianization homomorphism and mod out by the torsion subgroup). Lift the $r$ generators to $r$ elements of $G$: they generate a subgroup $H$. So $H$ is generated by $r$ elements, and surjects onto $\mathbf{Z}^r$, and hence the abelianization of $H$ is isomorphic to $\mathbf{Z}^r$.
To conclude, we need to check that $H$ has finite index in $G$. For this I claim more generally that
if $G$ is a nilpotent group and $H$ is a subgroup such that $H[G,G]$ has finite index in $G$, then $H$ has finite index in $G$.
If $G$ is abelian the result is trivial. Otherwise, let $G^k$ be the last nontrivial term in the lower central series, so $G^k$ is central and contained in $[G,G]$. By induction on the nilpotency class, we obtain that $G^kH$ has finite index. The $k$-fold commutator map induces a surjective homomorphism $\Lambda^kG_{\mathrm{ab}}\to G^k$. By an easy argument, the finite index inclusion $H\to G$ induces a homomorphism $\Lambda^kH_{\mathrm{ab}}\to \Lambda^kG_{\mathrm{ab}}$ whose image has finite index. Hence the image of $\Lambda^kH_{\mathrm{ab}}$ in $G^k$ has finite index in $G^k$. This image is precisely $H^k$. Hence the inclusion $H\subset G^kH$ has finite index. Since we obtained that $G^kH$ has finite index in $G$, we conclude that $H$ has finite index.
[Actually this argument through $\Lambda^k$, maybe suitably rephrased, is needed to prove the fact asserted by Derek that a finite index inclusion of nilpotent groups induces a finite index inclusion of the derived subgroups. It's true for all terms of the lower central series, and in a sense the most basis step is that of the last term (done above), where things can be linearized.]
PS. A better version of all this would be to control the index of $H$ in terms of the size of the torsion subgroup of $[G,G]$, and the Hirsch length of $G$ (or, more optimistically, the size of the torsion subgroup of $G$ and the nilpotency class of $G$ modulo its torsion subgroup).