"Quality" is a very subjective term. All of the whale watching tours in Juneau are "quality tours"... AND, they're all different. Each tour will take you from Auke Bay to an area (or 3) where humpback whales hang out. That's where the tours begin to differ.
The main difference between tours is the capacity of the boats they operate. Allen Marine and 4-Seasons (ship booked tours) operate large vessels with a capacity ranging from 100-150 people. Orca and Dolphin Jet Boat Tours operate 30-50 foot vessels which carry between 12 and 50 passengers each. You can also book a private or semi-private charter on a 25-40 foot vessel carrying not more than 6 guests at a time.
All tours will have snacks and refreshments available (although some charge and some do not.) Most tours will see other wildlife besides just whales. Often times the smaller boats can get closer to shore for a peek at seals on a rock, deer, eagles, etc. and the tour can follow your wishes much closer if there aren't 20-50 other opinions joining you - can you tell I'm a fan of the private chartered tours? ;-)
Some companies are starting to go beyond the basic Coast Guard safety requirements... I think it's mostly a marketing ploy as I've only seen news articles or witnessed "safety related problems" with one company. For the most part, all are good tours. It just depends what you're looking for.
-Case