Old English hu "how," from Proto-Germanic *hwo (source also of Old Saxon hwo, Old Frisian, Middle Dutch hu, Dutch hoe, German wie, Gothic hvaiwa "how"), an adverbial form from PIE root *kwo-, stem of relative and interrogative pronouns. Practically a doublet of why, differentiated in form and use.
How come? for "why?" is recorded from 1848 [Bartlett]. Emphatic phrase and how! is recorded from 1865. The formulation was common in book and article titles ("The National Debt, and How to Pay It"), but Pennsylvania writer Bayard Taylor, in whom it is first recorded, seems to have regarded it as a German or German-American expression.
Native American greeting, Siouxan (Dakota hao, Omaha hau), first recorded 1817 in English. But according to OED, the same word was noted early 17c. by French missionary Jean de Brebeuf among Hurons as an expression of approval (1636).