The Bloody Jack series by L.A. Meyer might be a great choice. They take place on an 18th-Century British naval vessel and follow Jacky Faber -- a ship's boy who is actually a girl in disguise.

I'm not sure who Cassandra Clare is, but two good historical novels are Kindred by Octavia Butler, and The Help by Katherine Stockett. I hope that helps.

Cassandra Clare has a young adult urban fantasy series that is really popular..Thanks for the suggestions!

A Great and Terrible Beauty by Libba Bray- Part of a series- may be more for girls than boys, though.

Prophecy of the Sisters by Michelle Zink is really good and has been fairly popular in my library and it's set in 1890s. Also Leviathan by Scott Westerfeld -- can't remember when it's set, but it's definitely steampunk genre. If you're not just looking for fantasy -- I would also recommend Annexed by Sharon Dogar which tells the Anne Frank story from her friend Peter's perspective.