We flew into Seattle one day ahead of the cruise and stayed at Inn of the Market. We did Pike's Market and walked down the waterfront for dinner.
We took the Amtrak train to Vancouver and stayed at Pan Pacific for four nights -- did the hop on/hop off bus and went all around the city, got off to explore Granville Island, Stanley Park, Chinese Gardens. Loved it all. Were sure to stop at a JapaDog stand for lunch one day.
After the cruise from Vancouver (our's was a 7-day cruise with a 12-day land portion to Yukon territory, etc.), we were flown back to Vancouver and stayed at the Fairmount at the airport.
The next day we took the Amtrak train back to Seattle and stayed four more nights at the Silver Cloud Lake Inn and took their free shuttle into the city each day. Be sure to do the underground tour -- very interesting.
We rented a car one day (the rental place was at a hotel within walking distance of us). We drove to the Lewis & Clark Center in Oregon so that we could complete our 50th state!
We loved everything about that experience and consider Seattle and Vancouver two of our favorite cities now.