They are busy in Asgard and or another planet, during the events of Ragnarok, the Third Thor film. This is hinted at in Civil War by Senator "Thunderbolt" Ross, when he asks where Hulk and Thor are, as if they were missing atomic bombs (funny, the US military has lost multiple atomic bombs).
Any further information is pending the films release, which will undoubtedly reference Civil War some way. But Ruffalo has stated in a tongue in cheek way:
“It’s an intergalactic buddy road movie with Banner and Thor,” Ruffalo told Entertainment Tonight at a press junket for his latest movie, Now You See Me 2.
The actor added fans will see “a lot more Hulk” this time around, doing what Bruce Banner/The Big Green Guy does best. When Now You See Me 2 costar Woody Harrelson asked if the Hulk will be even “Hulk-ier” in this new film, Ruffalo responded, “The Hulk gets Hulk-ier. The Hulk Hulks out. Hulk-ier and bigger.”
So, they were on a road trip.