It really depends what sort of tour you're after, and only YOU can decide... The Allen Marine tour will feature you and 150 of your closest friends on a ship about 65' long and 2-stories high.
Davey Lubin's tour is a smaller boat, and a much more personal tour of the area. Chances are, it will just be your group aboard, as I believe he maxes at 6 guests per trip.
The last time I was in Sitka (personal trip aboard the Can Can, not a charter or tour) we couldn't find puffins anywhere until we got to St. Lazaria Island. I don't suspect the Allen Marine tours get out that far, so it's a question to ask each vendor. I'm sure, if the weather permits, Davey Lubin will be happy to go wherever necessary if puffins are of interest to you. I also see the Esther G II is listed as having earned 4 stars (out of 5), so without seeing the vessel, I would still feel comfortable recommending the boat.
It all really boils down to whether you're the tour-on-a-motorcoach type, or the sort who travels and sees things a bit more independently, as a local would do it.
Happy Alaska Travels!
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