You can use the cheat that removes natives press F12 type in "Cortez' and hit enter

If it is the early stages of a trading post or colony the natives should be able to be attacked by an army in the province. When you select the army the info bar on the left should show a bubble that allows you to attack the natives. There may also be an issue in which your army is too small, but that is a theory.

If your colony no longer needs colonists because of its size the natives join or disappear altogether so the option to attack would not generate.