I have not fished either of these ports but have fished out of Kenai Peninsula launch sites a bunch of times. Halibut fishing is a blast, you will not regret it, especially if you haven't done it before. I would not go to AK and not go halibut fishing, the fish you catch will likely come close to paying for the charter fees at the $20-24/lb you typically pay for it here in Wegmans. Ketchikan and Juneau are in SE, which I believe is 1 fish limit, under 43" or over 80" for guided boat. Which means you're probably shipping home one under 43" for each person in your group. I'm sure you will have no problem getting your keeper at either port, they are not difficult to catch, but I would ask your question in the Saltwater Forum of Alaska Outdoor Forums, they will likely give you some ideas on which port might be better for various reasons, charters to recommend, other things to consider (length of boat ride to the fishing grounds, etc.),these guys are usually very helpful:
One thing to consider is whether the tides are more favorable the day you will be in Ketchikan vs the day you are in Juneau, how strong the tides are (stronger tides = more lead to get bait down = more tired forearms cranking up chickens and rebaiting,etc), time to be there to fish (they may leave port at 4AM for some tides, 6 AM for others, to get there ob both sides of slack tide, etc). Another is fish processing and means for shipping the fish home, I assume they have that at both ports, but you should check.
Feel free to PM me if you have questions