In Ketchikan, the first excursion is the Saxman Native Village and City tour, which goes from 9 to 11:30, and the second one is the Misty Fjords Seaplane Exploration, which goes from 11:45 to 1:45. I'm guessing it's probably not enough time. There is another Seaplane Exploration later in the afternoon.
And then in Skagway, the first excursion is Valley of Glaciers helicopter tour, which ends at 9:15, and the second excusion is the Eagle Preserve Scenic Float, which starts at 9:30.
It would be VERY tight on time. I am also assuming these are ship booked excursions?? You may also want to consider booking directly- savings can be significant. Especially for your choices- the Saxman Village tour booked at the dock visitor center runs about $25pp, Misty Fjords flightseeing has a definate advantage of direct booking- the tour allows a landing and the ability to get off the plane. I highly recommend the following venders I have gone with- Southeast Aviation, Carlin Air and Island Wings- about $185 (Southeast has early booking discounts). As for Skagway- book direct with TEMSCO air for your glacier helicopter landing. The Eagle float trip is out of Haines requiring a ferry ride- best operator is ECO Orca. Last season they had a 2 for 1 coupon with Family Circle magazine. http://www.alaskafloattrips.com/ If eagles are your priority- there are few sightings before the end of August and even then not in the numbers of photographs. Best sightings are after October- November.
So if the odds are not good for seeing eagles in late May, maybe we should reconsider taking a 5-hour tour to look for eagles? Is there much chance of seeing other wildlife on the rafting trips at that time of year? I thought it sounded like a nice, peaceful tour, but now that I think about it, it may also be a pretty cold ride in late May......?
There are a few eagles all year but no, you aren't likely to see many nor likely to spot other wildlife. But this trip is a great deal - especially like mentioned above- they offer 2 for 1 deals. A major consideration though would be to book the first trip after arrival then have a block of time to see Skagway. Be aware- the ferry route is the same as your ship takes in and out of Skagway. Late May the weather usually isn't that cold.