Both are grammatically correct but it would be more natural to say, "Before dinner, I had already finished my homework". "Had" indicates the action had been completed.

Both are correct and both sound natural. I think the sentence where you use the past perfect in both clauses would probably be used if you were talking about a time frame that was more distant than the time frame where you use the past perfect and the simple past tense.

I finished my homework before having dinner. I had finished my homework before having dinner. - These sound more natural.

Before I had dinner, I had finished y homework <= correct

I finished my homework before having dinner. I had finished my homework before having dinner. - These sound more natural.