By default, it's at course level - you have to export the gradebook from each course individually.
However, it's possible to write reports which combine gradebooks across courses; I've written one which combines grades from all courses in a category into one spreadsheet, and also one which simply allows one-click download of a zip file containing all of the individual gradebook exports from courses in a chosen category. Each was for a different purpose, and the combined spreadsheet probably wouldn't be of use to anyone except the department I put it together for - but the zip approach is probably generic enough to be useful. If you're interested in trying it out, I'm happy to send you a copy (with some brief instructions) - if you find that it works and is useful, maybe I'll consider releasing it more widely (i.e. via the plugins database).