With response times so short and critical, the obvious place for increasing security is on the ferry system itself, but anyone familiar with Washington State politics knows how likely it is that intelligent action will be taken there. As one ferry-riding poster mentioned above, the ferry system has already dropped much of the security it had installed after 9-11. The ability of those "Arabs" to recon the ferry and drive off in a vehicle with no license plates shows just how effective ferry security is.
I respect your assessment of the proximity of the ferry landing to the shipyard, and I generally respect your attempt to relate your concerns here. But you've demonstrated that you're uninformed as to the security employed by the Navy.
I remember in war games in the Marines I'd need to prepare threat assessments supporting operations and mission planning. As a newbie it was tempting to pile the maximum capabilities of everything on top of one another and present an unrealistic threat from a force, blocking off airspace to the maximum range of suspected SAMs, projecting ground forces from their most forward plausible location and giving them the capability of moving at their most rapid rate.
In the case of the Ferry, you appear to have it at its maximum capacity, taken over almost instantly, accelerating to its maximum speed to an aircraft carrier that may be the ship in the closest proximity.
You don't know what kind of patrols the Navy has to block access or what weapons are ready and trained on the entrance. You don't know how guards are trained and tested and you don't who has the authority is to fire under what circumstances.
You're free to warn people of what you know, but you're not qualified to assess the real danger until you have more information about the other side of the equation. And if you don't temper your estimate of the terrorist with an injection a lot more realism, you're not going to be believed.
There was a nurse here in October who was spamming any relevant thread with hysteria about what had to be done to protect against bio-warfare. She would have had us virtually shut down the economy. She was truly fear mongering. You're not as over the edge as her, but I think you're creeping a little in that direction.
I've spent all the time I can on this. I wish you well.