Hm that doesn't give you a lot of time. I was going to suggest getting a car for a day in Akureyri and driving to Myvatn (for loads of waterfowl and Gyrfalcon). However, that will be difficult to combine with a whale-watching tour from Husavik (assuming you're on the 10-1 sailing). If you push it you might get 1.5 hours to look around and tick the Dimmu Borgir Gyrfalcon pair. They do breed all over the country so you could get lucky anywhere, this is just a very reliable and well-known site.
Same story with Brunnich's Guillemot - the best sites I know off are at Latrabjarg in the westfjords (a 4-5 h drive from Isafjordur), and at the tip of Snaefellsnes (a 3 h drive from Reykjavik). Vigur holds Puffins and Black Guillemot, but not Brunnich's I'm afraid.
OK here is an idea: don't do the whale-watching trip when you're in Akureyri. There's a new company that will start up whale-watching from a RIB from Isafjordur in 2013 (
http://www.gentlespace.is/e_news.aspx?id=401) - looks pretty spectacular! There's not much else to do over there anyway (although the setting is ridiculously pretty) and you'll see the same whales and birds that you would around Husavik. If this doesn't work there are whale-watching trips from Reykjavik as well and they're pretty good (although not as atmospheric as they use new boats). How badly do you want to see Reykjavik? If you'd rather go out there's nice tours that can be done there; besides the whale-watching there is the spectacular (if touristic) Golden Circle, or you could soak in the Blue Lagoon.
Sorry I'm rambling a bit - in short: when in Akureyri get a car and do a day-trip to Myvatn, which will be great for the family (active volcanoes and stuff) and for birding (waterfowl & Gyrfalcon). Do whale-watching from Isafjordur, assuming the new company goes ahead. See Reyjavik and/or Golden Circle on your final stop, or take your last whale-watching opportunity.
Hope this helps!
N
P.S. you should see loads of whales from the cruise ship as well
P.P.S. you'll sail by Latrabjarg on your way south - maybe Brunnich's Guillemot at sea?