The case of "Native American Church v. Navajo Tribal Council" looked at whether the duties of the First Amendment on the government applied to Tribal Government. The conclusion was that the Tribal Governments are not part of the US, but subject to it. So the Constitution of the US does not apply to the US tribal regions, or to those under their jurisdiction, but Congress can pass bills that apply parts of the Constitution to the Tribal Governments. The first amendment does not apply to the Navajo Tribal Council, because Congress has not passed a bill that applies it.
The position of Native American tribes in the US constitution is hazy at best. There is the mention of "Indians not taxed" for the purposes of apportion, and the power of Congress to:
regulate Commerce with foreign Nations, and among the several States, and with the Indian Tribes;
Case law has generally taken the view that the Indian Nations are free to self-regulate; that they cannot form treaties with the individual States, nor with foreign nations, only with the Federal Government; that they have limited jurisdiction of non-Native-Americans even within their borders; and that Congress does have ultimate authority over the Tribal Governments.
So the second amendment would not apply, unless Congress says it does.