Learn Portuguese (Portugal): Quem são eles?

São is the "they" form of the verb ser (to be). Because the subject is eles (they), we must use the plural verb são. If the sentence was "Who is he?", it would be Quem é ele?.

Could I say Quem são elas? instead?

Yes! Both eles and elas mean "they". You use elas if you are asking about a group made up entirely of females. You use eles for a group of males, or a mixed group of males and females.

We are asking about multiple people. Does the word Quem (who) change to plural?

No, Quem always stays exactly the same, no matter how many people you are asking about. Only the verb (são) and the pronoun (eles) change to show that we are talking about more than one person.

Do I have to include the word eles in this question?

Not always. In Portuguese, you can often drop the pronoun if it is obvious from the context. If you are pointing directly at a group of people, you could simply ask Quem são? and it would mean the exact same thing.