Why is it that the Gardeners were able to rule their Kingdom for thousands of years, despite the fact the Reach has the same geographical limitations of the unstable Riverlands?

I don’t think it does, actually. 

To the south, the Reach has the Red Mountains giving it a pretty solid border, or solid enough that strategically placed Marcher Lord castles at the few passes across the mountains can contain the Dornish threat, or at least hold them up until the rest of Dorne can mobilize. 

To the north, the hills of the Westerlands basically meant that the coast road was the only way that the Westerlands could attack (unless they were going to invade the Riverlands first), and the Reach has Old Oak, Red Lake, and Goldengrove to act as its first line of defense there. (It also helps that the Riverlands were a failed state for much of this period, and so the Reach only had to deal with them for a limited time). Remember, the Gold Road postdates the Targaryen invasion, so that’s not as accessible a route for invasion, plus it dumps the Westerlanders out into the Riverlands, so there’s an element of early warning there too. 

And while their eastern border is a bit more porous, it’s not easy to march an army through the Kingswood. And the Stormlands were the Reach’s least numerous regional rival for most of that period, so less of a threat there. 

But on top of all of that, you just had much more effective governance. The Gardener Kings of the Reach (aided and abetted by the fact that their blood ties with most of the major Houses of the Reach created a common affinity) were for the most part incredibly good at binding together the Reach into an effective unit. Garth the Great forged the northern defenses with treaties, Gwayne the Fat brought the Manderlys and the Peakes into the realm with judicial decisions, Meryn III and Garland the Bridegroom used dynastic marriages to bring Oldtown and the Arbor into the Reach (giving economic, cultural, and naval might), and John II established the kingdom’s eastern borders. 

And that’s just scratching the surface of a House that, IMHO, has the best track record of effective monarchs in all of Westeros. 

Compare that to the Kings of the Trident, who never really managed to unite their kingdom or extend enough influence to their borders to feel comfortable enough developing their economy by handing out charters.