The Clipper has a number of instances in the winter when heavy seas force it to go slow, with green passengers cooped up for longer than the 3hr (normal) crossing. In addition, the daylight concerns will be even worse given sailing times and time on site.

I'd suggest 1 full day in dowtown Seattle. If you've done Pike Place and don't feel drawn to go back, then do other things. I've lived here for 20+ years and still have not seen all the sights. EMP, Pacific Science Center (Dead Sea Scrolls are still there, I think), the Bodies exhibit, visit the neighborhoods and just wander.

Take the second day and ferry out to Bainbridge. Explore the towns (by car) just on the other side of the sound. Ferry ride will be fairly short and the conditions much less an issue with those huge boats.

The last 1/2 day, visit UW.

Or if you want to see snow, take some time to drive out to Snoqualmie (1.5 hours away +/-) and frolic.

I know people have different ideas of what traveling is, but I know none who would consider spending 3 hours in a place and 8 hours getting there and back enjoyable.

And yes, do get a map.

Gardyloo.....again, you make the most sense.