I've done the Belize zoo on one trip and the Mayan ruins with river boat excursion on another trip. Hubby did the cave tubing twice. I don't think they still do that though. Enjoyed all, but have done our own thing since then. Be careful in Belize City. If you go outside the tourist compound, there is a local arts and crafts market that we really like. Just stay within sight of other tourists and do NOT go further than the craft market. Safety first. That said, I LOVE Belize.
Just keep in mind that "natural habitat" means something very different in Belize than in the US. There, they are already in thir natural habitat...the jungle. The zoo put up fencing and gravel in between and presto, a zoo! But, the cool thing is that you get a much closer look at the animals than you ever will here in the US. And some are critters I had never seen before.
Oh, you will really need insect repellant. Depending on the weather, but pretty consistent year round...it's a jungle with a lot of animals and that means lots of skeeters. I usually am not bothered, but that time I was glad to have my little bug repellant towelettes with me!
There is always the cave tubing, but the snorkeling in that area is exceptional. We went to Goffs cafe for a snorkeling excursion, great time. They actually gave you a guided tour of the underwater areas and pointed things out, it was wonderful! They also picked us up from the ship and dropped us off at the ship at the end.
They still do the cave tubing -- we did it a month ago. It was different and I enjoyed it. You wear a life jacket, and the water isn't very deep, so maybe your sisters would be ok. We all linked legs in our group, and the guide, guided our "train" and gave an informative talk about the Mayans and the spirituality of the cave. But if the sisters are really sqeamish about water, it's probably not for them.
I would book it through the ship, however, because the ship's excursions got the best tubes and the others looked like they had pretty big holes through which to slip. We also did the zip lining, but you have to be adventurous to do that and the walk up to the first platform can be rough for anyone not in good shape.
Just FYI, the state of the river, such as how much rain they have had recently, can affect the difficulty of the cave tubing. My hubby loved it, but there have been some accidents and he actually had to rescue a woman who got caught in a bad current. So, if your sister is not a swimmer, I would give this one a skip.