So let's assume that the not-for-profit is doing something we agree is ethical (i.e. a youth education centre or whatever). If they are doing something unethical, they shouldn't do it, no matter where the money is coming from.
So does the source of the money "taint" or change the moral-ness of what the not-for-profit is trying to achieve? Or is it in fact a good thing that money from a colourful character, by which let us say that it is coming from an unethical revenue source, is now going to an ethical place?
Is the not-for-profit perpetuating or enabling the unethical business of Mr Colourful? If yes, then it is unethical to take the money, because they would be part of creating unethical actions. If no, then perhaps it is not such a problem - I assume Mr Colourful's money is going to go somewhere, and it might as well go somewhere ethical.
How might the not-for-profit enable Mr Colourful's unethical business? Well, let's not assume that he places corrupt people in the not-for-profit - he is solely a source of funding and has no say, influence etc. whatsoever. But he might really like this not-for-profit idea and so want to create more revenue for it, which means that he will continue carry out his nefarious business practices with the not-for-profit as a reason. I don't know if the ethical/unethical business practices "balance out" in some mathematical way, but if there is a direct correlation between the two, I would say that it is not ethical to take the money.