Praise be to Allah.
The Standing Committee was asked a similar question, and they replied:
Working in a riba-based bank is haraam, and the one who does that is disobeying Allaah, but prayer offered behind him is still valid, because he is a Muslim. His prayer itself is valid, if he meets all the conditions and does all that Allaah has prescribed in the prayer, according to the more correct of the two scholarly opinions. If you can manange to pray behind someone else who is righteous and pious, then that is better. And Allaah knows best.