Unfortunately we have no authoritative text for understanding the references in the Qur'an which leaves many such references obscure. What we have instead is the tafsir, the exegesis that typically purports to explain the content of the Qur'an, often in reference to statements attributed to the companions of the prophet through a chain of transmission.

Tabari is a useful source of tafsir in regards to your question both because he's an early source (c. 838-923) and because he was happy to include multiple and potentially contradictory interpretations for a given verse.

That is the case in this instance. Tabari cites possible meanings for "كُنۡتُمۡ خَيۡرَ اُمَّةٍ" "You are the best community..." as including:

• Those specifically who made hijra with Muhammad from Mecca to Medina
• That if God had said "انتم" "You [pl.]" that it would have meant all of us, but he said "كنتم" and therefore meant specifically the companions of the prophet and those who came after them. (This is attributed to Umar ibn al Khattab)
• Or that it's all those who follow God's guidance from among his community.
• Or that it was the largest community that came to Islam.
• Or that it was simply the best community from among the people.
• Or that they were the last and best of 70 communities created by God.

So we certainly have a variety of options, of which both "all Muslims" and "just the companions" or "just the muhajirun" are equally plausible. The plain sense meaning of the word in question "umma", is often used today to refer to all Muslims, but of course that is itself an open historical question.

It's also worth noting of course that the tafsir itself is historically dubious and even religiously dubious. Ahmad ibn Hanbal, for instance, rejected the tafsir as unreliable. If we were to stick with the hadith, there "three best generations" reading certainly seems plausible. The hadith themselves, however, are historically dubious.

So TL;DR, we can't say for sure, and there are multiple credible readings.

Sourcewise: All of the above are my rough translations of Tabari, with the caveat that I'm at work and may have misunderstood a couple of them.