Is it better to cite a PhD thesis or an article under review?
Do you know if his article will be accepted? Would you know so soon enough? If there is a chance that it will be rejected (there always is but you may have a feeling of the quality of his article) I'd cite his thesis.

In any other case I'd cite his peer-reviewed article with Smith et al., under review or Smith et al., submitted to (name of journal). Papers are usually more accessible and perceived to be of higher quality than theses and it would also give him one citation on his article already.

Or, as Pont pointed out, cite both: Statement in your paper (Smith 2016 [this would be the thesis], Smith et al., under review [this would be the pending article]).