We did the Taku Lodge and Flightseeing excusion 4 years ago when my twins were 3. We did not do any other excursions that day, so I can't comment on whether it would be too much or not to do both of the ones you have planned. I can tell you, though, that the Taku Lodge excursion was worth every single penny and I would do it again in a heartbeat. The flight to Taku Lodge in the float plane was amazing. The food at the lodge was delicious. We saw several bears on the island up close. The excursion is not very taxing physically. There is an optional guided walk (with the 'bear bouncers' as we called them... two men with large sticks who were there to make sure the bears stayed a safe distance away) through the forested area. It was beautiful, and not strenuous. However, there were a lot of tree roots and such to step over... could be a concern for your parents. But if you choose not to go on the walk, just sitting outside of the lodge and staring at the water and the glacier is an awesome way to spend that time.
If you do feel the need to choose just one, I would go with the Taku Lodge excursion. There are many places to go whale watching (and honestly, we saw so many just sitting on the Wonder that we felt that part of our trip was fulfilled even without a specific excursion to do it). But seeing Alaska and the glaciers from the air and all the bears up close on the island... that's an experience that is much harder to come by. My twins celebrated their 3rd birthday on that trip, and now at 7 they still talk about the trip to Taku Lodge, the float plane, and the bears!
By the way, I was concerned beforehand about my 3 year olds on the sea plane because the seats are in a single file on each side of the plane. In other words, I knew I'd be able to sit in front or behind them, but not really beside them because the aisle goes straight up the middle. Having been on a float plane before, I knew how loud they are. I was concerned the noise would scare them (they give you earphones to wear, but its still loud). I even emailed the flight company ahead of time about my concerns, and they were super nice explaining how to best handle small kinds on their planes. It turns out that I worried for nothing. One of them fell asleep right after takeoff both ways, lulled by the sound and motion. The other one was so excited he could barely sit down. I sat behind him and held on to the loose end of his seat belt to make sure he stayed sitting. He really loved looking out the window at all the glaciers.