Most likely, "Base" Sasuke has more Chakra than "Base" Naruto. Sasuke has received numerous sources of chakra boosts (Itachi's MS, Hagoromo's chakra) that permanently increased his power as he upgraded his eyes. That chakra is always within him, regardless of whether or not he actually activates those eyes. On the other hand, Naruto's power-ups have come through mastering the ability to draw upon other sources of chakra (Sage Mode, Bijuu Mode, etc.). Naturally, Naruto's base chakra has not increased as much as Sasuke's, regardless of who can actually draw upon more chakra at will (hint: it's Naruto via BSM).
However, Sasuke still has less "stamina" than Naruto; Sasuke chakra is linked to his mental energies, whereas Naruto's is primarily linked to his physical energies (or Bijuu chakra). Therefore, all things equal, Naruto regenerates chakra at a faster rate than Sasuke does, even though Sasuke can access a larger amount of total chakra more quickly than Base Naruto can.
In the end, Sasuke cannot win a "Chakra War" against Naruto unless he (Sasuke) has the Bijuu under his control. Naruto simply has far more options when it comes to accessing vast amounts of chakra.
But yes, I would concede that "Base" Sasuke has more chakra than "Base" Naruto, although I'd caution that the term "Base" Sasuke is fairly meaningless; Sasuke's power is not based around increasing his chakra amount, but rather around channeling that chakra through his eyes. But yes, Sasuke has a huge amount of chakra.