To answer the Title, Its impossible to say. It appears you are asking if the Quincy are naturally stronger than Soul Reapers, simply because the elite of the elite Quincy, the Schutzstaffel, were able to use special tools to steal Soul Reaper Bankai's.
The Flaw with that logic is simply that we do not understand how the Tools work. We just know they steal Bankai once its been used in front of the tool, but not how they do it, or what the conditions are. The only clue we have is that Yamamoto was too powerful, so only Yhwach was strong enough to wield his Bankai. It could easily be that they are weaker, but like most supernatural/fantasy entertainment media, Most people can wield more power than their normal maximum, and even spontaneously power up permanently. Its very possible that there was no way without Voltstandig they could beat a Soul Reaper Captain in their Bankai State, yet could still wield the power of their Bankai. After all, the Soul Reapers do just that. By activating their Bankai, they are on average 5-10x more powerful than just their Shikai. The Voltstandig Transformation the Quincy use is very similar, and in fact they could not use it while they had a stolen Bankai.
To further nit pick, they too were granted power by Yhwach, as each one had a Letter, granting them not only more raw power, but also supernatural abilities. On their own, its impossible to say how strong they would be.
Lastly, There is one more thing to bring up, the first War with the Quincy. The Soul Reapers won that war, and almost all the Quincy were killed, to the point where Uryu and his father were the only known living Quincy left, excluding the Sternritter who may or may not be dead already.
Edit: Regarding your argument about zankaptou, there is also one thing to bring up. Yhwach's age is estemated at at least 1200 years, which includes the 1000 years he was mostly powerless. So, he was probably at least 200 years old by that account when Yamamoto Defeated him (using his zanpaktou). Though he could have been older than 200, he was still the first Quincy ever, which is pretty big here, because the Gotei 13 was founded over 1100 years before he was defeated. Yamamoto's Wiki Page in the history section brings up the founding of the 13 squadrens was 2100 years ago, 1100 years before yhwach's defeat, and the only picture we have of then, had several of the captians weilding zanpaktou. So, While Nimaiya may have been a captian back then, he had already invented zanpaktou, up to at least a thousand years earlier than the first ever quincy was born. A Soul Reaper without a zanpaktou is basically noneistant because they get one right after they become a Soul Reaper, and that was precident for hundreds of years before quincy existed, so there is no way to compare them. A Soul Reaper without a zanpaktou has also never been seen, besides Possibly Ichigo, so its impossible to say how powerful they were.