Hello
I have two environments
1. Develop
2. Production
To each of a separate domain.
I have SCCM 2012 R2 Server installed under development.
I want to install SCCM also producing
The question is what do I need to install.
Is secondary site or a new site?

It all depends on the requirements. Often dev and prod environments are completely separated. In a case like that you would require a new primary site in your prod environment.

What are the differences between them?

A secondary site has to be connected to current your primary site and a new primary site will operate completely separated.

Please read https://technet.microsoft.com/en-us/library/Gg712681.aspx

Secondary sites are about supporting client connectivity at remote locations; they have nothing to do with any other type of separation or scenario.