Is there sucha thing as a "best" 3d app to use with unity. Each one I have tried seems to fail on one point or another...mainly free ones of course but did try out Modo and C4D seem to have mesh or material problems wherever I go
Unity utilizes FBX exporters from all respected 3D programs that support it.
To be honest its a matter of personal choice in the end, find something that you are comfortable with and stick with it.
Something to be aware of, many of us eventually do not import materials from whatever application we are working with for your very reason. We just create our own optimized materials.