The Pacific Whale Foundation runs various whalewatching, dolphin watching and snorkeling trips for kids of all ages. Their focus is on marine research, education and conservation. Some trips include a complimentary "Watching Hawaii's Humpback Whales" color guide, a whale poster, and a Jr. Naturalist Program for kids. There are 2 ports, one in Lahaina on Front Street and one in Maalaea.
I found this 2.5 hour activity to be about an hour too long. Many of the younger kids began to suffer from boredom and/or seasickness (in addition to this parent). Keep in mind that we went at the end of whale watching season, but nevertheless seeing one-second glimpses of a whale from miles away was not the best way to keep a toddler engaged. I would recommend taking older children only, and only during peak whale watching season.
We just did this Whale watch in February and my 5yr old daughter had a good time. There was a moment when the boat got a little rocky and scared her a little but she loved seeing the whales. The boat was thankfully not very full, thus making it easy for her to see from any angle, but I think if the boat was full it would be a little harder to find a place for a small child to have a good view. The trip was just long enough for her attention span and she was ready to head back when we did. As an adult I loved seeing the Whales and saw MANY on our trip out. The price is very reasonable for what you get and the kids get a whale poster if you return to the gift shop.
The foundation offers educational tours via cruises, whale watching and snorkel trips. There are also day programs for children ages 6-12 and one geared towards preschoolers.