Generally speaking, the North / South route between Alaska (either Whittier or Seward) and Vancouver, usually has pretty calm water most of the time. The only time you are on very open sea would be the section North of Glacier Bay. Glacier Bay itself is a deep inlet - the ships go inside the protective bay and go back out - it is a whole day affair.
However, if you start your cruise from Seattle - then the section between Seattle and Vancouver can be rough.
Many people take their Alaska trips as a Cruise + land trip. You either do your land trip first then get on a cruise sail south, or do your cruise first and do the land trip after you disembark. My preference would be do the land trip first and then the cruise - mainly because the cruise would be a lot more relaxing versus the landtrip is always on the go.
As soon as you finalize your plan, I suggest you book your land lodging immediately. You have a lot more choices on pricing and availability.
When we did our land trip in 2001, I took the LAST available room at the desirable B&B at Healy (for Denali National Park) in April for our trip in Mid August, for example.
Last July when I booked the cruise (South Bound) for Sept 2 sailing, I immediately looked for hotel rooms at Anchorage for the 2 days pre-cruise. I was lucky to be able to find availability at Best Western near airport at $75 a night at the old wing. Same rooms at the new wing were over $110. Nothing below $150 in downtown Anchorage. Few weeks later, our hotel was sold out!
You can get a day pass for Anchorage bus system for $3.00. We decided to fly out 2 days earlier instead of 1 day as our flight schedule required connection at DFW in the evening, and if weather caused flight cancellation, there is no way we can make it to the ship if we fly out the next day.
The departure ports at Alaska for the South Bound cruise are at Whittier or at Seward. Whittier is 2 hours drive from Anchorage, plus the Tunnel with a fixed time table for car crossing. Seward is over 4 hour drive from Anchorage.