There's no natural rule specifying that only one thing may be at play. The reverse is often true - populations, particularly those of R-selected critters like muskrats, can suck up a few changes with little effect.
It's also worth noting that trends, by definition, are neither short-term nor localized.
Raptors certainly eat rats, but they're almost certainly not permanently driving populations on a continental scale.
Forget muskrats for a while. Say your car is running a little rough, so you take it to your mechanic and demand he replace the #3 spark plug. Never mind that you have no idea how cars actually work, or that you solicited the advice of a specialist, or that you could have fixed the problem yourself were it as simple as you postulated, or that you've never changed the filters and the muffler rusted off 40,000 miles ago; you simply won't be happy until he agrees it's that #3 plug and agrees to fix it for a couple bucks. Then sue him because your muffler is still rusted out.
Now back to rats. With a few notable exceptions, we've been driving this planet hard, ignoring the maintenance, and tossing our trash into the back seat, all the while proclaiming that simply funding this or that little problem will fix it all up. Ignore the whole anthropogenic climate change thing - hell, ignore atmospheric gasses entirely if that's what it takes to keep your hackles in place - and you're left with things like abnormally high levels of mercury in EVERY SINGLE FISH tested from AK to FL, abnormal estrogen levels in US waters, a whole lot of concrete, and simply how damned much of what you see out your window isn't native.
That is where the rats went, and where they'll continue to go as long as ignorance is a badge of pride in America.