The other plan, that the Washington State Ferries just squashed, would be to take the train to Tacoma, see the museum on my own, and then take a ferry to Seattle, but Tacoma has no ferries and the closest one does not go to Seattle. What's up with that?
http://www.wsdot.wa.gov/ferries/info_desk/route-maps/
[Please note I said "ferry/ferries" no fairies or fearies. Please keep your snickering to yourselves. :-P]