The MK/WL/FW boat operates until park closing and until all guests waiting at the MK dock after park closing need to get back.
The boat between CR/WL/FW may shut down earlier, but I don't know for sure. Except for ADR's, there's no reason for that boat to operate so late, since the MK boat will be available to get people from MK back to WL and FW.
We've ridden the MK/WL/FW boat many times between 10 PM and 1 AM.