In June there aren't going to be a lot of eagles there compared to fall. If a priority, you should be seeing most everywhere in Alaska, if you take the time to look.
Realize that if you charter a boat to Haines, you are sailing the Lynn Canal between Skagway and Haines, the same route as your cruise ship. Yes scenic, but if you are a first timer, and with a priority for Haines, taking the fast ferry may be a better option and included with some operators? Eco Orca is a good rafting outfit.