According to
the EEF/WHG/ANE autosomal analysis, Basques only have about 29% similarity with ancient "indigenous European" samples, if by "indigenous European" you mean "early hunter-gatherer" (WHG). That's a lot more than Spaniards (7%), sure, but it doesn't make them even top 5 among European populations, being beaten by the likes of the English, the Scots, the Norwegians, the Belorussians, etc. The Estonians, Finns, and Saami are probably the highest in WHG of all European populations, not the Basques.
If by "indigenous European" you instead mean "pre-Indo-European" then we can add the WHG and EEF components to get 89%--Basques have a lot of EEF, which represents the early Neolithic farmers. But 89% is only a little on the high side, with almost all of Europe hovering in the 80%-90% range, the notable exception being Sardinians, who are way up at 99%.
The fact that Basques have a large proportion of metal-age Y-DNA markers (extremely high R1b levels) is further evidence of their not being particularly "indigenous" in the sense of being from the Stone Age. It's also consistent with the fact that they have native words about metallurgy and agriculture
.