No, the earliest evidence makes her native Greek.

1. She first appears in a poem composed in the Aegean world ca. 700 BCE, the Hesiodic Theogony, at lines 274-281 (following Glenn Most's translation):

... and the Gorgons who dwell beyond glorious Ocean
at the edge towards the night, where the clear-voiced Hesperides are:
Sthenno and Euryale, and Medusa who suffered woes.
She was mortal, but the others are immortal and ageless,
the two of them: with her alone the dark-haired one [Poseidon] lay down
in a soft meadow among spring flowers.
When Perseus cut her head off from her neck,
great Chrysaor and the horse Pegasus sptrang forth ...

This poem is earlier than Greek settlement in northern Africa, so we can't imagine influence from African colonies at that date.

2. Her name, the names of the other Gorgons, the names of their parents Phorkys and Keto, and the word 'Gorgon' itself, are all Greek. Medousa is identical to a feminine participle of the verb med-: as written the meaning is 'ruling, protecting, providing for, contriving'. Gorgōn appears to be a back-formation from an older form *gorgōps, gorgōpos meaning 'rapid face, rapid looking'.

3. There is good reason to see strong influence from Mesopotamia and the Levant, however. Medusa herself isn't named in any earlier text, but the Gorgons do appear in Mycenaean (Bronze Age) depictions. Greek Gorgon iconography regularly show traits shared with the Mesopotamian Lamaštu, who is regularly portrayed holding snakes. Some later sources set the fight between Medusa and Perseus in Jaffa, in what is now Israel.

All that said, the basis for the idea of Berber origins -- I don't know what your source for this claims, so I can't address their claims directly -- is most probably an alternate version reported in Herodotus and some much later Roman-era sources that put the fight between Medusa and Perseus in Libya instead of in the Atlantic Ocean (Herodotus 2.91); Herodotus also reports on what he claims is a shrine to Perseus in Chemmis (a.k.a. Panopolis or Akhmim), in central Egypt. I'll let Lloyd's 1975 commentary on Herodotus book 2 speak on this (pp. 367-368):

Perseus had close affinities with Egypt through his connections with the Danaid Cycle ... These were doubtless quite secondary but were probably responsible for such developments as the Περσεύος καλεομένη σκοπιή ..., the association of the Gorgon with Libya (Schol. Pi., P X, 47; A.R., IV, 1513ff. with Schol. ad loc.; Ov., Met IV, 617ff.; Serv. ad Verg., Aen VI, 289) and that of Andromeda with Ethiopia (Apollod., II,4,3; Str., I,2,35 (C42); Schol. Pi., l.c.). From what follows it is clear that H[erodotus], or his predecessor(s), had identified P[erseus] with an Eg[yptian] deity. All available evidence indicates that it was Horus ... or Min-Hor ...

Now, the wealth of later sources that Lloyd cites certainly points to widespread acceptance of Herodotus' identification of the cult at Chemmis with that of Perseus. But two important points: (1) the earliest evidence points very clearly to Greek origins; (2) The route by which Medusa is tied to Libya is via a local Egyptian cult, not anything in Libya itself, so even if later reception of Medusa was flavoured with Libyan material, it wasn't genuinely Libyan but actually Egyptian.