I am making models in techne, and I need to use it in the mod. What is the best way to use the models in my mod? Should I export it in .obj or in .java. What is the best and the easiest way?

Look up Jabelar's tutorials.  They spell out how to do this clearly.

Ok found that, http://jabelarminecraft.blogspot.be/p/creating-custom-entities.html. I am actually using a block but that is not the problem. I just want to know if I should use the .obj export or the .java export. Why is .obj better?

I have never used the .obj export.  I have only used the java one.

 

Once you export it though, you are going to want to modify it heavily to do anything fancy for animations, or redundant objects (teeth for example, generate with an array and loop), setup child relationships to make the thing easier, ect.