I don't think the boats can take you. I don't remember ever seeing an ECV on the boat. I think stro;;er and such have to be folded up and carried onto the boat. It seems to me that their are steps to go down to get into the boat. On the other hand taking the monorail to get to MK is normally faster than the boat as it is the first stop whereas the boat stops at the Poly after GF. The way back is a different story however.
No, you cannot use the boat. GF, in my opinion, is not an easy place to stay and use your ECV. I stayed there in December and the Monorail was down a portion of every day. Every time the Monorail breaks down, it forces everyone with an ECV to use the bus. That means long waits for the bus in a very small bus waiting area. Sometimes when the Monorail breaks down the GF will add the bigger boat so that you can use that, but the problem is that you never know when or if they plan to do that. Often, you are trapped in a long waiting line for the Monorail and there is no way to try to get to the launch. It was a very frustrating stay for me using my ECV.
ECV's and the GF launches don't go we'll together. With an EVC the easiest transportation method is undoubtedly the monorail. All they do is roll a ramp to the monorail door and you drive right up. You don't have worry about causing a big commotion as happens on the WDW busses sometimes. Hope this helped!!