My vote is for Glacier Bay. Hubbard's awsome. Glacier Bay is better IMHO.
I must say however that on our two trips to Glacier bay the weather was perfect. On our trip to Hubbard the sea was pretty rough getting there and by the glacier was quite overcast although it didn't rain.
How great of an experience you'll have with the glaciers depends on weather and sea conditions on that day. On my cruise, we were able to get within 1/2 mile of Hubbard Glacier, and it was a beautiful sunny day, so it was perfect. But in Alaska, sea/weather conditions really aren't too predictable.
Know that whatever you pick, I'm sure that you'll have a fantastic time, so don't worry about it. Take a look at the other parts of the itinerary, and go from there :-).
I've only seen Hubbard and I thought it was absolutely amazing. We did have a beautiful day there, even the captain commented on that, said the last few weeks, the days there just were not that great, so we lucked out, got pretty close and heard and saw a lot, so that will be my favorite for a long time to come.