Releasing top-class products doesn't mean you're in a good position from a product development or competitive standpoint. It's merely a prerequisite for even being in the game - if a company can't produce a class-leading product (be it a body, lens or sensor) for at least one major photographic application, they're not even considered. That's why no-one mentions Olympus, Fujifilm or Samsung - without a full-frame camera system, they're not in the game.
Sensor quality matters a lot - Canon lost a lot of market share over the issue. So far, only Sony has released a high-resolution (for its time), high-DR sensor. Nikon and Pentax both use the older, 36MP version. They also make the 50MP and 100MP medium-format sensors used by a number of manufacturers. At high ISO, the A7R2's sensor also demonstrates great image quality at high ISO, competitive with the 1Dx2 and D5. Not to mention the A7S sensor, if you don't need the resolution - ample proof that Sony leads the pack, or is tied in front, no matter the DR, resolution or ISO requirement. Canon, so far, hasn't made a high-resolution sensor in the same league - the 50MP 5Ds sensor falls far short DR-wise, and performs poorly at high ISO. Nikon hasn't designed or made a high-resolution sensor at all - they're almost totally reliant on Sony for their better sensors. That's an ace in Sony's hands.
Nikon has the advantage in SLR AF systems. But how much of that can be translated to mirrorless systems? Sony leads the way in mirrorless AF technology, with Canon not far behind and Nikon not even in third place. To remain competitive for the next decade, they'll have to move in that direction, or risk becoming the next Nokia, stuck with old technology while everyone else moves ahead. After gaining a foothold with non-action shooters and Canonites frustrated with poor sensors, Sony is close to having a mirrorless camera capable of replacing an SLR for wedding, event and other general photography - indeed, for anything other than sports or fast action - and the D810 and A99 Mk 2 are likely more vulnerable than the 5D4 or D750. They're probably not too far off having a sports-capable system either - almost certainly, they'll be aiming to have one in the stands (likely als 8k-capable) in time for the 2020 Olympics, and the fact that they're in Tokyo will only make it a more important goal for them.
Nikon designs and makes its own lenses (some of which are great, some of which - particularly the zooms, which are the bread-and-butter of many photographers - aren't up to the standard of the latest Canon and Sony zooms), which is probably its greatest strength. But Sony has somewhat neutralised this by teaming up with Zeiss, at no cost to itself - being an optics company which doesn't make cameras and relies on other people's cameras to sell lenses, Zeiss' relationship with Sony is entirely symbiotic, rather than competitive or parasitic.
Yes, at the moment, Nikon is still ahead. But the momentum is in Sony's favour, and Sony also holds a better hand - there's nothing Nikon can do to slow down Sony other than developing and releasing better products, but far more that Sony can do to pile the hurt on Nikon should it find it in their advantage to do so.