Always depends on water levels, but the green ferry to MK does take ECVs. The smaller blue boat to the CR does not, unless you can dismantle and lift onboard.
The larger boat to MK will always be able to take your ECV barring a very few times that water levels do not permit - very seldom. The smaller boats that travel between the resorts (FW, WL and Contemporary) cannot.
To go to other parks, you will need to catch an internal bus to Outpost (front of FW) and board the designated park bus there.