Yes, the blue flag boat that goes between CR/FW/WL runs late, so you could go to WL, but I'm wondering why you want to? The transportation alternatives from both FW and WL are virtually identical (in fact, in some instances, shared).
If MK is open after your dinner, take the MK boat and get a BCV bus at MK.
If the MK is closed, but the Studios are still open, you would probably be better off taking the internal FW bus to the bus depot and then taking a Studios bus from there.
If both of those parks are closed, but Epcot is open (and provided you have a hopper pass you've used that day somewhere), you can take the blue flag boat to CR and take the monorail to Epcot. Then walk through Epcot to BCV.
If all the parks are closed, you would need to take the internal FW bus to the bus depot and take a DTD bus. Change buses at DTD for a BCV bus.
The main problem with the blue flag boat is that, unlike the MK boat, all strollers have to be folded up. Granted, they have to be folded up on the bus too, but the bus isn't moving when you're trying to get on board. It can be a little tricky, in the semi-darkness, to get on a bobbing boat with your hands full of toddler and stroller. I think the buses would be easier for you.
I'm assuming you aren't driving/renting a car? Otherwise, the simplest would be to drive to FW and just take the one internal bus back to Pioneer Hall.