My BSc. background is Material Science and Eng. I moved out for semiconductor and finished my Ms. in electronic Materials specifically in Shallow junction area in Silicon. I have applied for 2 Canadian university and one American University. The Canadians are top ranked however, American one is not ranked. It is a state university. I am wondering which one I should accept as the reputation of the university matters in career.

Reputation is fine after a PhD, but it probably won't help you during your time spent doing the PhD itself. I think you ought to make a balanced decision based on the facilities and the levels of support from supervisors. While reputation is a significant factor, I don't think it should be the only reason why you choose one uni over another.