The U.S. Border Patrol is part of U.S. Customs and Border Protection, and is responsible for patrolling the areas at and around international land borders.
Two recent USA TODAY articles discuss the increase of U.S. Border Patrol's presence on domestic trains, buses, and ferries, even on routes that do not cross into Canada or Mexico.
One article specifically discusses Border Patrol inspection methods in Upstate New York.
Read article: Border Patrol expands transportation checks
Read article: Some travelers criticize Border Patrol inspection methods