I know, from our trip a few weeks ago, that the larger boats allow you to roll the strollers right on, however on the small type boats(ex. WL to Cont)all strollers must be folded.
I'm not sure what type of boat crosses the water in Epcot.
Many yrs back, I remember getting into a heated conversation with a CM telling us to fold our double stroller - we had 2yr, 1yr and preg with #3. After riding the boat back and forth from YC to MGM and Epcot all week with stroller rolled onto boat, then one day CM will insists that stroller must be folded and since it would take a while to get kids out and stroller folded he would see us on the next time around. It was the contradiction we encountered that was so fusterating.
So this year with 2 single strollers and being able to wheel them onto the boats, my husband says hey Disney must have given up on folding all the strollers.LOL