What are pre-print repositories for math and physics alternative to ArXiv?
In mathematics and physics arXiv is by far the most used and reputable.

Of course, there are thousands other ways to self-archive your paper using not dedicated solutions (like personal website, GitHub, etc) and some general (like FigShare).

Yet, when it comes to pre-print services, they only one I am aware of is http://vixra.org/. It has policy of accepting everything; however, it has reputation of crackpotism (as arXiv is popular and editors rarely reject from it, so for the majority if researchers there is no reason to choose viXra (unless as a protest or something)).