I have a character that has not committed a crime, but is wanted by the Feds for questioning and whose mental capacity is in question (ability to make decisions for herself). If she can get on the ship - and into international waters - is she safe from their questioning?
She is now under the absolute control of the captain of the ship.
A likely scenario if the Feds know she got on the ship:
Feds contact cruise line and say: do you like being able to dock in US ports? Please have ship xyz come back to port (or just into US waters) so we can offload person xx.
Cruise line to ship xyz's captain: Do you like working for us? Please have ship xyz come back to port (or just into US waters) and in the meantime, please have person xx confined to quarters.
Check out Wikipedia's article on International Waters. Ships are generally under the jurisdiction of their flag country (country of registration). The problem with this overly general statement is that the laws relating to what is and is not claimed to be one nation's jurisdiction depend on the fairly arbitrary laws of that nation, as well as international treaties.
Your question lacks specificity. Important questions left unanswered: is she a U.S. Citizen? Which flag is the ship registered under? What is its next port of call? It's very unlikely that the ship will turn around (the costs both in time delays and fuel are too much). It is slightly more likely that a ship would detour to a near-by U.S. port (if there was one). If the feds were willing to helicopter in an agent or two, it's pretty likely that the captain would allow them to question her, depending on relations between the two nations as well as the captain's attitude.