I think that would work only if the agency took the billing. If they passed it through and Amtrak generated the card transaction (as is typical with airlines) it wouldn't qualify.
As a workaround, you can get the Chase Freedom, and buy Amtrak GCs at a store that carries the bonus categories. For example, Costco is currently selling them: http://www.costco.com/Amtrak-Vacations-$100-eGift-Card.product.100128241.html
That should earn 5x UR points/$ instead of just 2x.
EDIT: Oops, this is Citi, not Chase. But Citi does include gas stations in its bonus categories; any chance you can find a gas station selling those GCs?