Both words are good and can be used interchangeably.

Unfortunately, the word “church” has connotations in society and in religious contexts that are far from the original meaning for the word.

Assembly continues to have a meaning that is close to the original word that Christ and the apostles used. As such, “assembly” is preferable.

In the Portuguese language, the word “igreja” (church) actually comes directly from the Greek ekklesia. Unfortunately, it does have the same connotations as the English word “church.” The word “assembleia” is the Portuguese word that more closely reflects the meaning of ekklesia in the Bible.

This post is also available in PT.