For me it's one of two things:
1: The leads just seem really comfortable around each other. Their closeness doesn't feel staged, when they touch each other, even casually, it doesn't look uncomfortable or stiff. Their acting bounces off the other person's so it doesn't just feel like two people acting a scene, or two seperate people in a conversation that aren't really connected but are just sort of there, but two people that you happen to be watching while they do whatever. If they were to replace one of the actors with someone else, the show wouldn't be half as good, even if that other actor was just as good as the first one.
2: There's just this spark. The way they look at each other, the tension when they're close to one another, the way the air seems to bend around them while they stand in the same scene like they're the only two people in the whole world. This one is harder to explain for me lol.
Sometimes I sense both types of chemistry in one couple, but usually it's one or the other. I love them both equally though. I don't know if that was too long of an explanation but the idea of chemistry is really interesting to me so I love thinking about it and puzzling out what it is to me. I'm also curious how others would describe what chemistry is to them!