Someone said this earlier, but I don't see why their mandate would extend to only the milky way. They're trying to solve a general problem. The harvest is only a stop gap solution. Not the answer to their problems. And if they're asking general questions about synthetic/organic relations, it would seem that they would look for answers everywhere if they could (like other galaxies). But they don't have the capability.
If we accept that, though, then there's no reason why they wouldn't have expanded across the universe in the millions of years since their creation. I hardly think they'd stop at Andromeda.
And even if that were true, and they were in heaps of galaxies, why weren't the Milky Way races absolutely annihilated by an overwhelming number of Reapers?
I suspect that the writers at Bioware really don't want to address the Reapers ever again, given the mess of ME3 and Leviathan, and Montreal will want to do something else regardless. So... if they come up at all, I reckon it'll be handwaved that they are restricted to our galaxy.