A rec letter from people at management level sounds more convincing and mature. If you can't get it from your direct supervisor, you could try other managers who also know you very well.
My colleague is a senior manager, only inferior to the general manager of my dept. Do you think such a rec is OK? I just wonder if I have no recs from my supervisor, will it hurts my application?
i think hte senior manager is ok. The point is to get someone who can commend on your leadership skills and other qualifications that your peers are not in the position to commend. Schools do understand your concerns. You don't have to worry too much about that.