This is an interesting question. I don't have a full answer for you, as the Himalayas are quite a large region and I don't have detailed knowledge of its archaeology. However, a really mysterious society existed in the northwest part of the Himalayas (think modern-day Ladakh into Central Asia to the west and Dolpo and Mustang to the east) called variously Zhangzhung, Shang Tsung, Shangshung, Zan zun, and else besides (at least one source also claims its the inspiration for Shangri-la).

The political structure of Zhangzhung is still uncertain. It might have been an empire, a kingdom, or something less centralized such as a confederation or otherwise coalition-based territory. It certainly had sufficient power to undertake geographically extensive fortification projects, and numerous burial complexes have been associated with it (some with internment in the thousands). There are also extensive "standing stones" associated with Zhangzhung (and the broader region), though whether these were related to funerary rites or had other cultural importance is not certain. John Vincent Bellezza is one of, if not the, premier archaeologists of the region and it is my understanding he views these standing stones as separate in purpose from the burial complexes. Some Chinese archaeologists studying the region have argued they are perhaps not as distinct from burial complexes and rites as Bellezza would have them be. Regardless, the extent of the Zhangzhung polity to undertake various military and cultural construction projects was extensive. It may have then directly administered these vast swathes of territories (at least as 'direct' as geography and resources would allow) or it may have exerted more of a soft-power approach.

It's from its soft-power that much of Zhangzhung first came to us, prior to more recent archaeological undertakings, through myths and legends of the Bon religion. The Bon religion itself (a religion very similar in practice and theology to Tibetan Buddhism though predating it in some practices) and some contemporary scholars cite Zhangzhung as an early sponsor of Bon. As a result, it is featured heavily in many Bon myths. It may be, however, that the Bon tradition did not so much preserve the historical origin of Zhangzhung as it did appropriate it into its own subsequent origin story. I'm away from my books right now, and I'll check on this later, but it's my memory that David Snellgrove (very famous Tibetologist at the School of Oriental and African Studies) views Bon connections with Zhangzhung through a very skeptical eye. He does write that Zhangzhung's location in critical trade routes made it culturally cosmopolitan. The interchange of philosophical ideas (many probably brought by traveling yogis from India) likely helped prepared the way for later dissemination and adoption of Buddhism. His interpretation, if I'm synthesizing two of his writings correctly, is that these early cultural interactions between yogis and Buddhist aesthetics from India with the region's pre-Buddhist religions gave rise to a nascent Bon religion in Zhangzhung. When Bon itself is described as a pre-Buddhist religion in Tibetan history by writers such as Snellgrove then, what it refers to is not pre-Buddhist in an absolute form (as in, predating Siddhartha), but predating the Buddhist revival in Tibet around the 9th-10th century C.E.

This risks getting a bit off track. To summarize, one group of peoples in the Himalayas are those of Zhangzhung. Zhangzhung is still steeped in myths and legend, though through 20th century archaeology and linguistic studies more is coming to be known of it. Its location on (and probably control of) important trade routes meant it was exposed to diverse cultures. In turn, these cross-cultural interactions gave rise to the Bon religion, though to what extent Bon as it exists now existed then is uncertain. The importance of Zhangzhung to modern Bon could be based on accurate oral histories, or it could be the result of retroactive continuity centuries later by Bonpos contesting the growing Buddhist influence on Tibetan elites and seeking to establish territorial, historical, and philosophical legitimacy and continuity on par with Buddhism.

Sources:

Mark Aldenderfer and Zhang Yinong, "The Prehistory of the Tibetan Plateau to the Seventh Century," in The Tibetan History Reader (Gray Tuttle & Kurtis R. Schaeffer, eds.): 2013.

David Snellgrove, "Rulers of Western Tibet," in The Tibetan History Reader (Gray Tuttle & Kurtis R. Schaeffer, eds.): 2013.

David Snellgrove, "Himalayan Pilgrimage," 1981.

John Vincent Bellezza's website on Zhangzhung archaeology: http://www.thlib.org/bellezza/

Wikipedia on Zhangzhung: http://en.wikipedia.org/wiki/Zhangzhung

I don't have an answer myself, this is FAR outside my area of study, but there is an AMA on Tibetan History hosted by /u/Xtacles on March 25. If this thread doesn't yield results, you might try fielding the question at the AMA.