I have cruised Alaska multiple times and I just returned this week from a back to back cruise in Alaska.
The difference between an Inside Passage cruise and a Gulf of Alaska cruise is that generally the Inside Passage cruise is usually a roundtrip cruise. On most every cruise you will hit Ketchikan, Juneau and Skagway, however on a roundtrip cruise you may hit Sitka and some of the cruise lines are now trying a couple other ports.
For what it is worth I feel a Gulf of Alaska cruise that takes you all the way between Vancouver and Ankorage is the best choice. I feel you miss the best sites when you do a roundtrip cruise. The roundtrip is beautiful but IMHO the best sites are past the Inside Passage. On a Gulf of Alaska cruise you will hit Ketchikan, Juneau and Skagway and either Seward or Whittier depending on the cruise line. You than go from Seward or Whittier up to Ankorage, or do the reverse.
Which cruise line does the best job? Most every cruise line does a good job in Alaska, so you can pick which you like best. Princess and Holland America have been there longer than anyone else and both do a great job. Princess and Holland America will always use a pier, with the exception of Sitka, but the others may tender if there are to many ships in Port.
My personal favorite cruise line in Alaska is Princess but that is my preference.