The word order in Korean is not fixed, so as a rule both of them are correct.
If you ask me which one is more natural, then I'll answer
어제 영화 재미 없었어요.
그저께 날씨 좋았어요.
is more natural.
(어제 영화가 재미 없었어요, 그저께 날씨가 좋았어요. is also right, but Koreans usually drop '가' in these kind of sentence.)