I'm looking to book a 4 day on the Dream in Jan. Since it's a short cruise we wanted to go to WDW for 3 days after. Can you book a package through Disney or do you have to book them separate?
You can! What you'll want to book is called a Land & Sea Package. You'll find some preliminary (and booking) information here, and you can ask ANY questions you might have here on the boards, where I'm certain some of our "seasoned" cruisers will be happy to help!
A few of the people on here have done both and I'm sure they can help you with any questions you have
Given the choice, I would opt for going to WDW first so that you can relax on the cruise after the hussle & bussle of the parks.
Jon and I had this discussion the other day when we were discussing a Disney Cruise - he had the same thoughts as you. Good to know.