Well, if you want to see Glacier Bay you're far better off getting yourself to Gustavus (which is served by AS in the summer; search for GST). Haines has no Glacier Bay cruises that I am aware of. From there, Glacier Bay National Park has a vendor that offers day cruises into the park, which combine wildlife and glaciers but definitely focus on glaciers. I've done it and really enjoyed the trip; Gustavus is a neat little community as well.
You'd be wise to google the NPS website for Glacier Bay National Park.
Alternatively, you could also do a separate whale watching cruise that departs from Juneau. Bottom line is that if you want to get to Glacier Bay, you need to go to Glacier Bay itself, not try and do it from Juneau in a day.