Liquid Snake is definately a bottom and he is so angry about it. He thinks he should be a top, because that's more masculine, but he got all of Big Boss's recessive genes. Liquid resents and feels emasculated by Solid Snake, because, as he got all the dominant genes, he's obviously a top.

As for Solid Snake, he's definately a bottom. This causes some issues as his boyfriend Otacon is also a bottom, but they make things work.