Should he work for a company whose boss is a kaafir?

Your
earnings and your work have nothing to do with your boss’s situation or his
not praying or his listening to music or watching haraam things. You should
keep on trying to advise him without getting too close to him, because there
is the fear that he may influence you. 

You also
have to apply the rulings of sharee’ah with regard to your boss, if he
continues to neglect prayer – such as not initiating the greeting of salaam
with him and not liking him in your heart. We have already discussed a great
deal about the rulings on not praying and the fact that it is kufr
(disbelief) and riddah (apostasy). 

Shaykh
Muhammad al-Saalih ibn ‘Uthaymeen said: 

We advise this brother who works with kaafirs to look for a job where there are no enemies of Allaah and His Messenger, who follow religions other than Islam. If that is possible, what is how it should be. If that is not possible, then there is no sin on him because he is doing his job and they are doing theirs, but that is subject to the condition that there should be no feelings of love or friendship towards them in his heart, and that he should adhere to the teachings of sharee’ah with regard to greeting them and returning their greetings, and so on. Also he should not attend their funerals or their festivals, or congratulate them on the occasion of their festivals. (Majmoo’ Fataawa al-Shaykh Ibn ‘Uthaymeen, 3/39, 40).

 And Allaah knows best.