Right now, he's both.
Secret Avengers has been going on for a while now, so it definitely doesn't happen after AvX. And Wolverine and the X-Men is happening before AvX as well, since there will be AvX tie-ins soon.
The complex relationship between when a comic is published and when it occurs chronologically is often confusing, such as with Spider-Island and Wonder Man's assault on the Avengers. In this case, it's very simple. Beast works at the Jean Grey School for Higher Learning during the day and moonlights as a Secret Avenger whenever he is called on by Steve Rogers.
In the conflict between the Avengers and the X-Men, my assumption is that Beast will definitely NOT be on the X-Men side. Since Cyclops is leading the fight against the Avengers, it seems unlikely Beast will find his cause sympathetic, due to their recent falling-out.