I'm not familiar with Sitka Secret personally, but a fairly good indicator of the quality is whether or not they appear on the current list of 5-Star Safety Rated vessels at http://www.mxak.org/fivestar/5star.htm
All of these smaller boats (mine included) are not subject to any required inspection by the Coast Guard. Some boats "go the extra mile" to do a VOLUNTARY inspection each year (that says a lot right there) and then they are rated on a scale of 1 to 5 in terms of how much optional (but great to have if you needed it) equipment they carry.
I know many locals that would never even consider chartering a boat unless it had earned all 5 stars in that program, but I realize that some businesses are small and can't afford or choose not to carry all of the equipment necessary.
All other things being equal, I think I'd resort to "the list" and pick the highest rated boat I could find.
Happy Alaska Travels!