I guess the terms is so new that its definition is evolving. From what I've been exposed to, "gender" and "sex" (as a biological state, not the thing you do in the bedroom) are the same thing. Sexual orientation is who you prefer to have sexual or romantic relations with. Gender identity or sexual identity is your "mental sex." Those are three different concepts.
Absent qualifying words or context, "sexual minority" and "gender minority" have their obvious meaning - someone who is of a biological sex that is neither a majority nor, if there is no majority, a plurality. Technically speaking, either males or females are probably a majority or plurality, leaving everyone else a minority. Practically speaking (and absent high levels of gender-specific childhood deaths e.g. female infanticide) males and females are approximately equal in numbers, so calling either one a "gender minority" is kind of silly. That leaves those who are neither unambiguously male nor unambiguously female.
You can legitimately argue that those whose gender identity doesn't match their body are also gender minorities if you take the view that the brain (vs. the mind) has a "gender." One day this will be "settled science" but I don't think it's quite there yet.
However, I don't think you can make the same argument about a person who is male or female: A gay man is almost always a man in his genes, in his reproductive organs, and in his head. A lesbian woman is almost always a woman in her genes, her reproductive organs, and in her head.
Another distinct concept is the group of people who are disenfranchised or dis-empowered merely because of their gender, gender identity, and/or sexual orientation. You don't have to be a minority to fall into this category: In many parts of the world females are technically a majority but hold relatively little political power.