I'm sure someone else will correct my information if it's not accurate, but it seems a good many of our fellow Polynesian fans are taking a weekend break!
I'm not sure what you are describing when you say a "swim bubble". The marina does make standard life vests available to you. These life vests come in all sizes and are suitable for the little ones, too. It's been many years since my babies needed them, but we used the life vests for a few years and they were great!
You will, most likely, have to remove your child from the stroller to board the boat. Whether you will be required to fold it is another variable--depends on the number of guests boarding with you and the space available. I have seen folks just carry child and stroller onto the craft and park it behind the wheelhouse. If the captain permits you to do that, just be aware the stroller will be in motion without locks engaged!

At Disney, I've found that some of the captains follow the rules stringently, others not so much--just luck of the draw. Personally, I would fold the stroller and hold the child--it's more of a safety issue for me.
Hope that helps you in some small fashion. BTW, welcome to the boards
one disney baby!