It depends on what sort of story you're looking at. American Girl Publishing puts out an entire series of books based on historical events. There's also the Dear America series, published by Scholastic, and that includes the new books about famous princesses such as Elizabeth I, Mary Queen of Scots, and the Czarina Anastasia. Carolyn Lawrence's Roman Mysteries are published by Puffin. If you're looking for lighter fare, Mary Pop Osborne's books come from Hyperion, I beleive. Nearly all publishers of YA books also have stand-alone historical fiction titles that are not part of a series.
I'd recommend picking up a copy of the new Children's Writers and Illustrators Market (2006) and looking through it to see which publisher(s) might be the best target for you to query.