You can find this on the level "A Train to Catch", which is level 10.
This one is kind of hard to describe exactly. Towards the end of the level, there will be a stack of crates on top of a plateau on the mountainside to the left of the train tracks. Blow those up, and the ark will be inside. If you're looking at this plateau from afar, the game will actually load the ark before it loads the crates so you'll see a golden glow on the mountainside.
You can go for this after you destroy the AA turrets on the train. Follow the tracks and you will fly past another town, and then the train tracks will start to "snake" up the mountainside, turning first to the right and then back to the left and then right again. Before the track turns another sharp right after that is the plateau, on the left. Like I said, a little hard to describe.
It would be right before the train that's going to ram your train shows up, but you should fly there long before your train gets there to give yourself time to search.