What is the ruling on the money of a wage earner who works in a lawful scientific field, while knowing that his employer's money is usurious (obtained through interest-bearing bank loans)?

It is not permissible to deal with someone whose entire wealth is certainly known to be unlawful (haram), because that leads to consuming unlawful things and assenting to them. If a person is destined to work with him, he must ensure that his wages come from lawful (halal) money. If this is not possible, then it is not permissible for him to work with him. As for unlawful wages, they must be spent on general Muslim welfare, or given as charity to the poor, and it is not permissible for the employee to benefit from them. This is if all the money is unlawful. However, if lawful and unlawful money are mixed, then that has a different detailed ruling.