The location of Kever Rachel was still known at the beginning of galus bavel as Rashi brings down on Breshis 48:7 that Rahel Imeinu was davka buried there so Am Yisrael could go pass her tziun on the way to Bavel. If the mesora of the tzium was preserved for hundreds of years until then, it’s not such a stretch to assume the location was known 70 years later when the galus was over and even more so after people started coming back.
I’ve heard several theories that the site known today isn’t valid but it’s from academically minded sources – I’ve yet to hear a Torah based svara. For example I’ve heard that the real location is in Adam or another that it’s in the north, however the pasukim are pretty clear that it’s a parsa from Beit Lechem in Efrat. There are those who want to say there have been multiple ancient locations named Beit Lechem but again there is only one area known as Efrat so it doesn’t make sense to assume it’s a Beit Lechem other than the one there.
Yeshiva News has reported on Rav Kanievsky visiting the site so presumably he holds it’s the right one, and there was a story about 8 years ago involving Rav Mordechai Eliyahu davening there and having a gilui of Rachel Imeinu so it would seem he held it was the right location as well. Between Bayis Sheni and the rule of the Turkish Sultan I’m not sure if there are recorded sources of the mesorah but it would be something interesting to look up.
I usually reference kevertzadik when looking for kivrei tzadikim – one of their guys does a lot of research into the sites.