I wouldn't take a little one on it.
First, you're expected to stand the entire time. there are two window wells with metal rails around them. (There are two very small benches towards the front of the ship, but it's difficult to see anything from them.)
There's a strong smell of deisel fuel. I noticed some of the others covering their noses.
The ship rocks a lot. I'd be concerned that a toddler would have trouble keeping her balance. I'd also be afraid around the rails. It would be very easy for a little one to crawl through one and fall down the window well which is recessed in the botton of the boat.
You make two stops. One is at an established reef, one is at a developing reef. Yes you see some fish, but it's not exactly teeming with them.
The guide is very nice and I did enjoy hearing about the area. Other than that, I'll admit, it was pretty boring and I wasn't thrilled with standing, rocking and leaning.
Bring a pail and shovel, grab a spot with an umbrella and I think your little one will be a lot more entertained.