In most law schools, it takes a full semester course to explain the complexity of the legal system in this country related to Native Americans. The "tribes" are considered nations for some purposes but not for others. For voting, however, both Puerto Ricans and members of the tribes are U.S. citizens, and reservations are considered to be part of the state or territory in which they are located.
Both major political parties allow the territories to vote in the presidential primaries. However, the Constitution of the U.S., do not allow voters residing in the territories (other than D.C.) to have a vote in the electoral college. And no, it is not fair. Many other democracies -- Canada, Australia, and even Israel -- allows citizens residing in their territories to vote in the general elections for parliament.
It's particular unfair regarding Puerto Rico as the last two referendums (2012 and 2017) had majorities for statehood and Puerto Rico is larger (both in raw numbers and in terms of the number of representatives that they would be entitled to) than any current state -- beyond the original 13 -- at the time of statehood. While some challenge the validity of the last two referendums in terms of participation (a critique that would invalidate most U.S. elections), there is a simple solution. The process for statehood has three parts: 1) Congress invites the territory to draw up a state constitution and offers to admit the territory as a state; 2) the territory then has a constitutional convention to draft a state constitution which is then ratified by the voters; 3) upon finding that the state constitution meets the conditions in the offer to admit the territory, Congress grants statehood. For Puerto Rico, the ratification vote can include a turnout condition and a separate vote of accepting the offer of statehood.