I have cruised Alaska multiple times and I will be returning next year to cruise Alaska again. It is my favorite cruise destination.
As far as which cruise line is best that would depend on what you prefer for a cruise line. Princess and Holland America have the most experience in Alaska. My personal preference is Princess.
As far as the route if you are just doing a cruise and not a land package I would go from Vancouver up to Ankorage. IMHO if you do a roundtrip you will miss some of the best scenery that you can see from a cruise ship by turning around to go back to Vancouver. Seeing this is the Carnival section of the board I believe that the Spirit is the only Carnival ship at this time that does this.
If you are looking at a land and sea package I would take the land package first and cruise back from Alaska to Vancouver. The land portion can be hectic and tiring and you could relax on the cruise back.
Alaska is an amazing place to see and to cruise.