First off, let's establish this: Native American Tribes were independent and are still sovereign nations to this day. The United States has recognized this through hundreds of treaties, Supreme Court cases, and even the U.S. Constitution. They had their own governmental structures, their own religions, their own stratification, philosophies, sciences, understanding, languages, and some had writing systems.

Regarding the portion of your question for after the U.S. Revolutionary War, a number of tribes were more powerful than the U.S. The U.S. relied heavily on preserving and restoring friendly ties with the natives both during and after the war in order to preserve their newfound republic. The first treaty they made was with the Delawares in 1778. In addition to forming an alliance, establishing travel and borders, and an exchange of supplies, Article 6 even offers the tribe a place in the U.S. Congress:

. . .and to form a state whereof the Delaware nation shall be the head, and have a representation in Congress: Provided, nothing contained in this article to be considered as conclusive until it meets with the approbation of Congress.

At such an early point in U.S. History, practically any tribe would have posed a serious threat to the United States.