I have seen a certificate course in lingoda and Goethe-Zertifikat course. Which is accepted by a company or university as proof of German language and which one should I prefer?
You should prefer the certificates offered by the Goethe-Institute. The acceptance of a language certificate really depends on the company or university, especially concerning the level. Ask before you apply. But as the Goethe-Insititut is the official institute for language and culture of the Federal Republic of Germany, their certificates have the highest reputation.
If you only want to study, you can also take the testdaf exam. It has five levels, and level 4 allows you to study at almost every university. More information: Site of the testdaf