There is no "best" for everyone since "best" is relative. Some would say "best" is longest, some will say "best" is whichever one offers the largest discount, some will say "best" is something else.
Have you checked the small boat tours from Saltwater Lodge? Probably the least commercial. If you do a kayak trip to Aialik Glacier, that doubles as a Kenai Fjords tour so you don't "need" to take a separate Kenai Fjords tour, though some people certainly have done the tour twice on one trip.
Probably the least commercial would be to hire a boat with a local fisherman BUT then that would be pretty pricey and they aren't always the best tour guides. While commercial sounds negative, they usually do offer the best value for a tour - and I would also choose a tour with a ranger on board - they would offer you the most reliable information. I haven't done that tour for quite a few years, otherwise I would offer specific recommendations. :)
I love being on a smaller boat with a max of 15 passengers alaskasaltwaterlodge.com/alaska_whale_watchi…
Dont know if you'd like this, as it is a commercial boat, BUT, the Kenai Fjords Glacier Tours are not overcrowded. The captains are very knowledgeable. The scenery is amazing. the tour is long enough. And at the end of the tour, they dock on Fox Island (in Resurrection Bay). and give you one hell of a buffet, with chocolate cake too
hope this helps
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