I've done both. For us, driving was faster, even with having to wait for the bus.
That said, the boat ride from MK to the Fort was so relaxing and enjoyable. Plus, there is the bonus of not having to worry about the alcoholic beverages.
If you go to the late show, there are buses to take you back, but they can take a while as they make multiple stops. If you are at the first resort, then great. If you are at the fourth or fifth, it could be quite tiresome.
If the weather is inclement, or the time is really important to you (particularly after the show), then I would suggest driving and taking the internal bus.
If it's a lovely evening, take the bus to MK and enjoy the boat ride to the Fort.
Also, as has been mentioned, allow plenty of time no matter how you travel. If you are early, you can always take in the wonderful relaxing atmosphere of the Fort.