Well considering both your options both are pretty safe and good if you know what you are doing.
Ill gives you some tips and examples.
(I bought my emerald green controller off ebay and its a real nintendo one)
If you are buying off of controllerchaos i am almost certain you will be just fine.
Ebay on the other hand will need some help and looking out for.
First up:
This is
FAKE:
This is
REAL:
As you can see. the biggest difference is the "Nintendo Gamecube" logo near the top middle of the conntroller.
Another thing is that pictures that look like they just came off of google images are most likely fake.
And of course. ALWAYS and i mean ALWAYS check the sellers reviews and location. You can never be too sure.
And my final note. Check for the box if it says that "For Compatible Gamecube" first off makes no sense and second it is fake.
Hope I helped!