If you want Glacier Bay, then your choices are already limited.
which is GOOD!!
I also will assume you are looking at a round trip cruise??- for clairfication all Alaska cruises are "inside passage" (you wouldn't get to Juneau or Skagway without it). Focus less on the ship and most on time in ports, route, price. My favorite time is mid to late August, shoulder season rates, good amount of daylight, still decent weather. BUT weather is never guaranteed, so forget about worrying about it, prepare for it instead.
I always book my air independently and never would consider cruiseair. Just be aware you will have to do your own transfers.