You could fairly accurately say that a form of (limited) Martial Law was instituted in the 1864(?), N.Y.C. ,Civil War Draft Riots (The Five Points War), when the U.S. Navy shelled lower Manhattan from naval vessels in the harbor and regular army toops staged a march, to demonstrate contol, through the Five Points. That was the deadliest riot in all U.S. history.
Again in the wake of the S.F. Earthquake, as noted,and in ~1968, in the Detroit and Newark riots and finally, in post Katrina N.O., there were "imposed" instances of Martial Law, e.g. Federal troops as police, wholesale disarming of civilians, Shoot-to-Kill orders where arson or sniping was suspected. I do not count the use of Federal Troops to enforce school integration , because those actions were taken to enforce lawful orders of the Courts vindicating Civil Rights.
Other than the Whiskey Rebellion and under Reconstruction, in the sucessionest States, those are the only instances of Martial Law I can remember in U.S. history. Albeit, I'm sure I've missed a few. Query if you should count the use of the Army in the West after the Mexican war, against Native Americans in the Indian Wars and against the Huks, et al in the Phillipines Islands. Those were American territory, but won by conquest?