Dwarf, pygmy, midget, manikin, homunculus, runt are comparable when they mean an individual and usually a person of diminutive size.
Dwarf is the general term not only for a human being but for any animal or plant that is definitely below the normal size of its kind; often the term suggests stunted development.
Pygmy originally was applied to one of a race of fabled dwarfs mentioned by Homer and others; now it is used especially of one of a people of small stature found in central Africa.
In general application the term carries a stronger connotation of diminutiveness and a weaker suggestion of arrested development than dwarf; when used in reference to a person, it often implies relative tininess, sometimes in body but more often in intellect.
Midget stresses abnormal diminutiveness but, unlike dwarf carries little suggestion of malformation or deformity; the term is applied usually to a tiny but otherwise more or less normally shaped person exhibited in a circus or employed in place of a child in theatrical performances.
Manikin is often applied not only to a dwarf but to any human being who for one reason or another seems despicably small or weak. Often it suggests an animated doll.
Homunculus usually suggests even greater diminutiveness and often greater perfection in form than midget; it is the specific term for an exceedingly small artificial human being such as was supposedly developed by Paracelsus, a famous Renaissance alchemist.
Runt, usually a contemptuous designation, applies to a dwarf or undersized person, especially to one who is conspicuously puny or undeveloped.
The term is also applied to an animal, especially a domestic animal, small of its kind; and it is used specifically of the undersized one of a litter (as of pigs).