The boat is slooooow. Allow about 45 minutes, including the wait. I would be at the boat dock by 4:45.
I think there are a couple of better options:
1. Drop the car off at POR in the morning and take the bus to MK, then take the bus from MK to DS (the bus starts running at 4:00,) and then take the boat to POR after your dinner.
2. Drive to MK in the morning, then drive to DS, then drive to POR.
Unless you really want to go to POR between MK and DS, it's an unnecessary step that's eating up a good chunk of your park time.
And I'm not sure if you realize this, but if you really want to check-in in person rather than online, you can do so as early as 6:00 am. You don't have to wait until 3:30.