Is the journal indexing by SCOPUS meaningless? A journal that I want to submit my manuscript is SCOPUS and WoS indexed (Q3, impact factor: 1.89, SJR 0.264, Fee: around 1000$). But my Professor said SCOPUS indexed journals are MEANINGLESS!(two months ago he said SCOPUS indexed journals are also OKAY). 

He prefers SCI-indexed journal which is Q3, impact factor:0.7, SJR:0.224, Fee: around 250-300$. I understand, maybe SCI index is a little bit higher than SCOPUS but if you scale SCOPUS(IF:1.89) and SCI(IF:0.7).

Which one is better to publish in?
Scopus is quality-curated, i.e. getting indexed by it is not meaningless. 

However, it is not as selective as the Science Citation Index, which remains the gold standard. 

Therefore you are better off publishing in a SCI-indexed journal if you can. Arguing with your professor is unlikely to be a good idea in any case - they have much more experience than you and will have a better idea where to send your manuscript.