It is not clear what language the autochthonous inhabitants spoke.
If the theory is correct and there weren't any major shifts, Lithuanians autosomally do not match Uralic speaking populations.
So the theory regarding the language is that even during Mesolithic the inhabitants of Lithuania spoke some sort of proto Indo-European (inasmuch as they were a type of Northern Indo Europeans who arrived to these part of the world with the first post-Ice age migrations).
Narva culture who also lived in the Lithuanian territory, however in different locations than local autochthons, were different anthropologically (they might have likely spoken a variant of proto-Uralic). The later wave of immigrants were the Corded Ware who were again Indo-Europeans, but already of some Southern Branch. Their language was also a version of proto-Indo-European.