It's a map, either hand drawn or official. The map could be coded in such a way that only Tuco understands it.
Earlier on before the bridge explosion and the drunk captain, Tuco pulls it out looks at it and says to Blondie,
There should be a bridge across that river.
Also the way he folds it when he tells Blondie to trust him indicates that the paper is very large so it's not notes. The only type of document you fold that way is a map.
The scene where he throws it away indicates he know longer needs the map as he is at Sad Hill Cemetery. Blondie told him the name of the grave was Arch Stanton as well.
Remember Tuco knows the location of the cemetery, Blondie knows the name of the grave.