In reply to Alan M: I did a sea kayaking trip across PWS back in 1994 from Whittier to Cordova over 2 weeks - as part of an Operation Raleigh expedition.
Amazing place, lots of wildlife - from mossies to bears.. slightly scary crossing the inlet up the valdez with monster oil tankers coming up/down
mail me if you want some more information, although as i said it was semi-guided so I didn't have to deal with any of the logistics of getting kayaks there etc
not sure how easy it would be to get up high and onto alpine terrain from your kayaks, seem to remember a lot of steep forested slopes at sea level
you could maybe stay a night in the log cabin we built for the forestry service on Green Island!