Hi, the boats from the Poly do only go to the MK. Then they go to the GF and back to the poly.
If you want FW, you take the boat to MK and take a FW boat from there.
I believe the Poly boats stop running an hour after park closing. They stop promptly - maybe not even an hour after park closing. I know we tried a few times to take the boat instead of monorail with no luck. They were done for the eve. Monorails run much longer than those boats.
Boats from the Polynesian go to the Magic Kingdom and the Grand Floridian. The boats operating times change with park hours. The boats will continue to operate an hour or so after park closing.