Magneto was MIA in the movie Logan. Chronologically, he was last seen near the end of Days of Future Past, in 2023. It would seem he hasn't seen Charles, Logan, and the X-men since then.
We have no idea where Magneto or any of the other mutants are. As far as we know, they're probably dead.
For starters, Logan was a movie about Logan, not Wolverine, and not the X-Men. The rest of the world's mutants were purposefully left out of the movie because they were irrelevant to the point: Logan's final journey of discovery.
However, there are clues scattered in the movie that might explain where everyone else is. First of all, there's multiple references to the "Westchester Incident" (not all by name), where Xavier
killed 7 mutants and injured many other people.
Westchester is the location of Xavier's mansion, where the X-Men HQ is, so we can extrapolate from that the likelihood that Xavier
killed several of his own X-Men and probably fled into hiding.
There is also a short clip from a radio talk show near the start of the movie, in Logan's limo, where the callers says something like "it's 2029, why are we still talking about mutants?". This implies that, to the average person, mutants are a thing of the past.
Finally, one of the Reavers remarks to Caliban that he "used to track muties" for them. From this we can probably guess that the Reavers used to hunt down "dangerous" mutants for Alkali, and the fact that he stopped could mean there just aren't any left worth hunting down.
However, there is one small twist near the end of the movie:
Alkali won't send the Reavers into Canada after the children, who believe there's a safe haven there.
So it's possible that the remaining mutants have merely fled to safety and are in hiding elsewhere, we just don't know.