Along with his brothers John and Brigadier General Robert Swartwout, Samuel was a close ally of Aaron Burr in his early career in New York State politics.
After Wilkinson took command of New Orleans in November, Swartwout was one of four Burr allies he arrested for misprision of treason and sent to Washington, D.C. for trial.
This position had great importance, as the collection of customs in New York was one of the largest sources of income for the United States federal government.
The recess appointment was upheld by the United States Senate on March 29, 1830, giving Swartwout a full term of four years.
He held meetings in New York where Stephen F. Austin, Branch Tanner Archer, and William H. Wharton appeared in quest of funds and supplies.
After he left the country, or perhaps before, his account was "adjusted" by a subordinate and possibly by his successor, through the instigation of President Martin Van Buren.