Giant Rat of Sumatra by Sid Fleischman

After being shipwrecked Edmund was saved by pirates. Nicknamed Shipwreck by the captain, he becomes the cabin boy for the pirate ship. The year is 1846 and Shipwreck is about to return to North America for the first time in almost two years. Anxious to return home to Boston, he finds his plans may not go as he hopes. The United States has declared war with Mexico and San Diego will soon be in the midst of battle. And Shipwreck is an American. Now he is the enemy. Will his Mexican captain be willing to protect him?