In addition to Luca's nice suggestion, one might consider other constructive foundations such as $IZF$ (abbreviating "Intuitionistic Zermelo Fraenkel") or the more explicitly constructive $CZF$ (abbreviating "Constructive Zermelo Fraenkel") set theories.
$IZF$ incorporates the notion of `construction' via the use of an intuitionistic metatheory, whereas $CZF$ in addition to an intuitionistic metatheory has the following properties:
(i) Separation is restricted to bounded formulae.
(ii) Replacement is replaced by the following `Strong Collection Scheme':
$\forall a [\forall x \in a \exists y (\phi (x, y) \rightarrow \exists b (\forall x \in a \exists y \in b \phi (x, y) \wedge \forall y \in b \exists x \in a \phi (x, y))]$
(iii) Power Set is replaced by the following `Subset Collection Scheme' which allows us to construct the set of all definable subsets:
$\forall a \forall b \exists c \forall u [ \forall x \in a \exists y \in b \phi (x, y, u) \rightarrow \exists d \in x (\forall x \in a \exists y \in d \phi (x, y, u) \wedge \forall y \in d \exists x \in a \phi (x, y, y))]$
Where $c$ is not free in $\phi (x, y, u)$
Further, there is $KP$ (for Kripke-Platek set theory). This theory (though the metatheory is classical), restricts the subset collection scheme to $\Delta_0$ formulae (and so respects the idea of `constructing' subsets out of absolute formulae).
In addition one might consider the Univalent Foundations Project, which brings together some of the type-theoretic considerations mentioned by Luca with homotopy theory to provide a foundation that is more constructive in flavour. Unfortunately, I don't really have the knowledge to say any more than Luca; but should you be interested there is a collaborative book available for free:
http://homotopytypetheory.org/
Further, there is a completely different approach that might be of interest to you. Recent work by Linnebo and Studd has yielded modal set theories, where the notion of building up the layers of the cumulative hierarchy is treated more seriously. We add modal notions $\Box$ and $\Diamond$ which are to be read as "no matter how far the hierarchy is continued it will be the case that" and "the hierarchy can be continued so that". While their aim is not constructive, it certainly could be appropriated by a constructivist, where each $V_{\alpha}$ is thought of as being added in a constructive process.
Details of $IZF$ and $CZF$ can be found here:
http://plato.stanford.edu/entries/set-theory-constructive/index.html#1.3
http://plato.stanford.edu/entries/set-theory-constructive/axioms-CZF-IZF.html
A short discussion of $KP$ is available here:
http://plato.stanford.edu/entries/settheory-alternative/#ConSetThe
The Homotopy Type Theory book is available from:
http://homotopytypetheory.org/
Linnebo and Studd's work is contained in the following papers:
Studd, J. P. (2012). The Iterative Conception of Set: a (Bi-)Modal Axiomatisation. Journal of Philosophical Logic :1-29.
Linnebo, Øystein (2010). Pluralities and Sets. Journal of Philosophy 107 (3):144-164.
Linnebo, Øystein (2013). The Potential Hierarchy Of Sets. The Review of Symbolic Logic, 6, pp 205-228. doi:10.1017/S1755020313000014.