The first one is correct. "Was came" does not exist as a verbal form and "had came" would be "had come" but would still be the wrong past to use.

The first one.

Hey Eshwah, Yes, only the first sentence is correct. Since the second sentence is in the past tense as well, it is wrong to say "was came", you could just use "came". If you wanted to use "had" in your sentence, that would mean you need to use the past perfect tense. Then the sentence would have to have a "had" + "past participle" part in it. The past participle of "come", is "come". So you could say the third sentence as "My uncle had come yesterday with his family." Hope this gives you a clear idea.

I agree with Francesca. "Came" is the only verbal form that you have provided that conveys an action that began and ended in the past.