Well, some of the coldest times in my life have been on that boat ride to the MK in the winter. Here are some tips:
1) As others above have said, it's kind of hit or miss. It could be in the low 70's in the morning, or it could be in the low 30's, there really is no way of guessing with Florida weather, as the cold comes and goes. Your best bet will be to check the weather starting about a week out from your trip up until your trip, and plan accordingly.
2) If you can get inside on the larger boats, do it. It will be much warmer, it's sealed, and you won't have any kind of wind in your face.
3) If you can't get inside on one of the larger boats, try to sit in the back compared to the front. You won't have the direct wind in your face, and you will be somewhat shielded.
4) If you're on one of the small boats, you're pretty much exposed no matter where you sit. However, the middle of the boat seems to be a bit less exposed than the front or back.
5) If you are sitting in an exposed area, the more you can sit on the inside part of the seat (closest to the walkway), the more shielded from the wind you will be. The outside edges will be the most exposed.
As I mentioned, some of my coldest times have been on that boat trip (although the coldest is normally coming back from the Contemporary after the sun has gone down, brrrrrrrrrrrrr). I'm a Florida native, so I probably get a colder than you northerners (but I can handle the heat just fine!!

), there have been quite a few times where I've had to wear multiple sweatshirts/jackets/etc... to stay warm, and sometimes it seems like the trip will never end....lol.
All in all, it's one of the things that's great about the Fort in winter, you'll have fun!