Unsupervised domain adaptation generalizes neural retrievers to an unseen domain by generating pseudo queries on target domain documents. The quality and efficiency of this adaptation critically depend on which documents are selected for pseudo query generation. The existing document sampling method focuses on diversity but fails to capture model uncertainty. In contrast, we propose Uncertainty-based Iterative Document Sampling (UnIte) addressing these limitations by (1) filtering documents with high aleatoric uncertainty and (2) prioritizing those with high epistemic uncertainty, maximizing the learning utility of the current model. We conducted extensive experiments on a large corpus of BEIR with small and large models, showing significant gains of +2.45 and +3.49 nDCG@10 with a smaller training sample size, 4k on average.