Capt Larry / Orca Enterprises is a great choice for whale watching and can arrange for a drop off/pickup at Mendenhall.
Ketchican is nice to walk around, the Lumberjack show is kind of hokey but fun. The Misty Fjords flightseeing trip with Michelle at Island Wings is an excellent choice. but can get pricey
If you haven't been to Skagway before I'd stay there rather than head down to Haines. The catameran ride down/back is the same channel your ship sails so you won't see any different sights. Also I don't think the eagels are really there in big numbers until late Sept/Oct. IMHO a much better option is either to rent a car and drive into the Yukon or take the longer train/bus trip. The shorter 3 to 3 1/2 hr trip doesn't get nearly as far into the nice scenery.