Something astronomical is probably your best bet. Meteors are good, but like you say they're not a sure thing -- even if you get some good hits on your planet, it doesn't ensure an extinction-level event like what you want (note that "extinction-level events" don't necessarily mean that all life ceases to exist -- otherwise our own planet's biosphere wouldn't have continued through 6 previous events!).
To get a lengthy period between events, you'd need your "extinctor" object(s) to be on highly elliptical, very large orbits. We're already familiar with lots of these in the form of comets -- Haley's Comet being probably the most famous, returning every 75.3 years.
But if we have a big object that comes around and smashes into the planet, that's it -- it's not repeatable. And comets' tails just don't have the "killing power" necessary to pull off an extinction (well, they might, but they'd most likely have to expend too much of their mass in each pass to be repeatable for long).
So we're probably looking for an object that effectively "radiates" death.
We could put a particularly massive object into our highly elliptical orbit. If it's big enough, it could inflict cataclysmic tidal forces on the planet, pulling tectonic plates apart and triggering gigantic earthquakes and mass eruptions all over the surface, effectively wiping out most life and certainly devastating any civilization that might have built up.
The obvious answer here then is a Jupiter-sized -- or bigger! -- gas giant. On the other hand, passing so close to the sun may cause the latter to "suck up" too much of its atmosphere, and we again have the "crumbling comet" problem. So a stony giant planet may be a better bet.
Now, people are going to see this thing coming from a long way away -- we can already see Jupiter with the naked eye, and it's so far away our own tiny little moon has more influence on our tides! Maybe that's what you want, but I've got something else in mind.
It's one thing to see a big dot in the sky growing bigger and bigger until it passes so close that it destroys you. It's quite another to see something you can't even describe, let alone understand, do the same thing.
Can you imagine what you'd think if you saw the stars in your sky doing this:
You'd see this bizarre, mysterious, and terrifying effect moving ever closer and closer, affecting more and more of the sky, until eventually your world is destroyed amid earthquakes and volcanic eruptions. One heck of a terrifying harbinger of the apocalypse, eh?
You might think this is a black hole, and in fact you would be right. Just don't get caught up in the popular hype about black holes "sucking in" everything in sight -- outside their event horizon, they're basically no different than any other massive body. They just happen to be so dense that their surface (if they even have one) is lower than the point where their gravity is so intense that light itself can't escape -- but it can and does bend around it, creating the "lensing" you see above!
To make it more mysterious, you could call it a Dark Star instead. They were a legit theory under Newtonian physics, though apparently Relativity means they've basically been replaced by black holes as the consequence of a super-dense object; if your society goes extinct before they discover Relativity and/or Quantum Mechanics, but after Newtonian Mechanics, they would likely theorize a dark star rather than a black hole. Plus, it's a scarier name than the over-done "black hole" (just my (not-so-)humble opinion).
You can put this thing on just about any orbit you want to achieve your apocalypse at any interval. If it isn't in sync with your planet's orbit, you'll have variable degrees of the apocalypse on each pass, growing more and more devastating until it peaks and then becomes less and less devastating -- but always plenty to wipe out civilization and leave only scattered survivors on an almost unrecognizably changed landscape.
And for bonus points, your civilization could reach the early space-faring stage, and so long as they can't escape the solar system to colonize another there's nothing they can do to save themselves -- after all, this is literally a second sun coming to wipe them out!