There is no "best", just which might best suit your priorities - budget, itinerary, size, amenities, etc. I've done Alaska on Holland America and Princess (on the delightfully small Pacific Princess - our favorite!)
I prefer glaciers to ports so a day sailing in Glacier Bay is an important priority to me. They limit how many ships can get permits to sail there, so not all do - check!.
Sailing round trip from Seattle is usually cheapest for flights (for Americans, at least) but since most Alaska cruises are 7 days, you lose ports or scenic sailing if you start as far south as Seattle. One way cruises (usually Anchorage to Vancouver or reverse) tend to have more time in port & scenic sailing.
I really don't like people, so would not go on a large ship (and to me, anything more than 1500 people is too large
) But the smaller ships are rare and therefore more expensive.
What the large ships offer are a lot more onboard amenities - entertainment, kids clubs, extra specialty dining venues. These are not things I care about, but given the rest of the cruise landscape, my husband and I are clearly in the minority
Alaska is gorgeous - I've been 3 times and cannot wait to visit again! For us, a land trip combined with a cruise is the best of both worlds - we were spoiled last time as we had family living outside Fairbanks - we visited, drove from Fairbanks to Anchorage and boarded our cruise there - had a fantastic 2 week trip, saw lots of wildlife etc (there are many packages offered by cruise lines if you do not feel able to plan a land trip on your own - but it's pretty easy! And usually cheaper to DIY)