It is very difficult to find a paper of Hurwitz dealing in any way with the geometry or topology of $\mathbb{H}^3/PSL_2(\mathcal{O}_{\mathbb{Q}(\sqrt{-D})})$. (And I am not sure I like what this implies about our ways of keeping knowledge alive, attribution and such.) The closest two things I could find were the following:

- A paper of Bianchi on computations of fundamental domains for $PSL_2(\mathcal{O}_{\mathbb{Q}(\sqrt{-D})})$:

L. Bianchi. Geometrische Darstellung der Gruppen linearer Substitutionen mit ganzen complexen Coefficienten nebst Anwendungen auf die Zahlentheorie. Math. Ann. 38 (1891), 313-333.

The main purpose of the investigation seems to have been reduction theory (and classification) of quadratic forms. The description of the fundamental domain is based on explicit generators for the group. The discussion of the topology is based on Poincaré's hyperbolic space model, the explicit transformation formulas for the group action, and the metric of hyperbolic space.

On page 2 of Bianchi's paper there is a reference to

A. Hurwitz: Über die Entwicklung complexer Grössen in Kettenbrüche. Acta Math. 11 (1888), 187-200.

That paper is mostly about continued fractions and discusses what could possibly be interpreted as related to the fundamental domains for $PSL_2(\mathcal{O}_{\mathbb{Q}(\sqrt{-D})})$ for $D=1$ and $D=3$. It seems, however, to be a rather indirect link of Hurwitz to cusps.

- Next, there is a 1892 paper of Bianchi:

L. Bianchi. Sui gruppi di sostituzioni lineari con coefficienti appartenenti a corpi quadratici immaginarî. Math. Ann. 40 (1892), 332-412.

In this, he states the relevant theorem: "Il numero dei vertici singolari eguaglia il numero delle classi degli ideali nel corpo quadratico corrispondente." Singular vertices for him are orbits of boundary points (or boundary points in each fundamental domain), and it seems to me that in §§2 and 3 he essentially proves this result by computing the orbits of $PSL_2(\mathcal{O}_{\mathbb{Q}(\sqrt{-D})})$ on the boundary projective line (as already suggested in various comments).

There is a reference to Hurwitz's work here as well:

A. Hurwitz. Grundlagen einer independenten Theorie der Modulfunctionen. Math. Ann 18 (1881), pp. 528-592.

For some reason this paper does not seem to be in MathSciNet. Anyway, Bianchi says

"Ma senza riferirci al teorema generale di Poincaré daremo qui
una dimostrazione diretta di questa proprietà affatto analoga a quella
che il Sig. Hurwitz ha fatto conoscere pel gruppo modulare."

Meaning that Bianchi's computation of the fundamental domain does not make use of Poincaré's general theorem, but is proved directly analogous to Hurwitz's arguments for the modular group. Hurwitz's treatment of fundamental domains for the modular group and its congruence subgroups on the upper half plane (in the abovementioned paper) seems to consider only the upper half plane, and not discuss boundary points.

Conclusion: At least from these two findings, it seems that Hurwitz was not directly involved in the proof that cusps for the Bianchi groups are in bijection with ideal classes. Maybe additional information could be inferred from Hurwitz's mathematical diaries which are available from the ETH library.

It is not clear to me if Bianchi really did consider the topology of the orbifold. He considered the group $PSL_2(\mathcal{O}_{\mathbb{Q}(\sqrt{-D})})$ (or $PGL_2$) as generated by an explicit set of transformations, and he viewed the group action on $\mathbb{H}^3$ in terms of explicit formulas. From the papers above it seems he did not think about an orbit space, but just about the construction of some fundamental polyhedron which contained representatives for all orbits. From this point of view, of course, cusps and the quotient topology are not an issue at all since everything takes place in $\mathbb{H}^3$ or $\overline{\mathbb{H}^3}$. (The same applies to Hurwitz's treatment of the action of the modular group on the upper half plane.)

In any case, in view of the above references it seems to me more appropriate to credit Bianchi (in 1892) with the identification of cusps and ideal classes.