In this case we're lucky that Herodotus and Xenophon are not our only sources and spoiler: Xenophon is definitely the outlier, which is unsurprising since Cyropaedia is not a reliable source for Persian history, nor is it really intended to be. Instead, it is a political treatise and a historical romance - something I've written about before. Most modern historians do not dwell on the issue, but they tend to side with Herodotus, broadly speaking.

There are four basic versions of the story told in five ancient sources:

1. Herodotus' Histories 1.205-214 and Justin's Epitome of Pompeius Trogus 1.8-9: Cyrus was killed in battle with the Massagetae (called Scythians by Justin/Trogus) on his northern frontier in the Central Asian steppe. The warrior queen, Tomyris, captured and decapitated his body and immersed it in a wineskin filled with blood.
2. Berossos' Babylonaica 3.5: Cyrus was killed in battle with the Dahae on his northern frontier on the eastern shore of the Caspian Sea.
3. Ctesias' Persika Fr.43 from Stephanus of Byzantium: Cyrus was wounded by a javelin from an Indian elephant-rider while fighting the Derbikkes on his northern frontier in Gandhara and was taken back to camp to deliver his last will and testament to his sons before succumbing.
4. Xenophon's Cyropaedia 8.7: Cyrus died peacefully in his sleep at Babylon after giving his last will and parting advice to his sons.

There are four more relevant sources that do not deal directly with Cyrus the Great's death, but instead discuss his tomb. One is naturally the tomb itself - the physical mausoleum still standing at Pasargadae. The other three are Strabo's Geographica, Arrian's Anabasis Alaexandri, and Plutarch's Life of Alexander, all of which discuss Alexander's visit to the tomb.

All of these are important because they help refute one of Herdotous' claims (and the claims of Trogus/Justin who repeated them). Very clearly, the Massegetae did not capture and keep Cyrus' body. All of the sources for Alexander's visit describe the experience and none of them even hint at the idea that Cyrus had been decapitated or otherwise disfigured. In fact, several of them comment on how well preserved the body had been in wax, suggesting that Cyrus's corpse was transported back to Persia before decay could really set in.

However, the very existence of the mausoleum and the splendor described by the Alexandrian sources also refutes Xenophon who wrote on of Cyrus's final wishes as:

Now as to my body, when I am dead, my sons, lay it away neither in gold nor in silver nor in anything else, but commit it to the earth as soon as may be. For what is more blessed than to be united with the earth, which brings forth and nourishes all things beautiful and all things good? I have always been a friend to man, and I think I should gladly now become a part of that which does him so much good.

Not only was this obviously not what happened, but it is actually at odds with what we do know about Persian burial customs more generally. All of noble tombs we can identify, or even theorize about are built from stone and elevated from the ground. Most of them have evidence for an elevated or sunken place to set the body/bodies within the tomb structure. If we extrapolate a little further, Xenophon's Cyrus is horrifyingly at odds with traditional Zoroastrian burial customs, which see burial directly in the ground as polluting a sacred element. Of course, there is lots of debate over whether or not to count Cyrus or any of his successors as "real" Zoroastrians, but it is worth noting that Herodotus' describes the Magi as practicing an early form of Zoroastrian excarnation and all of the Persian kings do seem to have taken steps to avoid direct contact with fire, earth, or water upon their deaths.

Then there's the issue of Ctesias and Berossos. Neither is usually considered a very reliable source for the early parts of their histories, and the surviving parts of the Babylonaica are barely long enough to be useful. However, both were working with traditions otherwise unknown to the Greco-Roman world. Berossos was a Babylonian priest in the 3rd Century BCE with access to ancient Babylonian records. Ctesias was a Greek physician in the court of Artaxerxes II and contemporary to Xenophon who pulled much of his information from oral traditions at the Persian court. Unfortunately, he also privileged the juiciest and most dramatic versions of those traditions over the most accurate accounts. Still, both of them were working much more directly with stories of Cyrus' death than Herodotus and have less dubious motivations than Xenophon.

It would be great if Cyrus's tomb had been preserved like the best Egyptian counterparts, but it was unfortunately pillaged not long after Alexander's visit, leaving us to speculate based on the sources above. Ultimately, given the minimal variations between the three stories of violent death and their relatively proximity to primary sources, it seems Xenophon's account is not historical and is intended to fit in with his larger romanticized image of Cyrus.