An alien, in the broadest sense, is someone or something not native to where they currently are. In the common sense of most fiction, though, it means anything originating from an extraterrestrial source.
Contrary to Hollywood, not all aliens have long heads and mouths on their tongues. Although some will scare the ever-loving crap out of you anyway.
In many Transformers continuities, in addition to humans and Cybertronians, there are both organic aliens and robotic aliens. Many of the organic ones look very human, and an awful lot of the robotic ones have the ability to transform like Cybertronians. The extent to which these similarities are coincidence varies from species to species, when it's explained at all. Aliens (besides Autobots and Decepticons) popped up infrequently during the second season of The Transformers, but played a far larger role in the third and fourth seasons. The Beast Era saw the introduction of the Vok, a species of energy-based creature. Depending on your point of view, Botanica's beast mode (mobile plant-creature) is an alien as well.