Hi, Amy! I am a Walt Disney World fanatic, so I would say there is no bad time to go! I do have times that are my favorites, and I try to make trips with my family during those times.
For us, October is a great time to visit. EPCOT has the fabulous Food and Wine festival, and my girls like to go to the World Showcase to sample cuisine from around the world. They also love Mickey's Not So Scary Halloween party! They get to dress up in costume, trick or treat, and have a blast!
Another wonderful time is just after Thanksgiving. The holiday decorations are up throughout the theme parks and hotels. There are all sorts of holiday offerings, and my girls love heading over for some gingerbread right from a life size gingerbread house!
I much prefer staying onsite. You can park your car and leave it for the length of your vacation if you've driven, or you can fly down, take Disney's Magical Express to your hotel, and leave the transportation for the rest of your stay to the capable team in Disney Transportation. Onsite also gives you Extra Magic Hours - these are hours where the theme parks are open only to Walt Disney World resort guests. There is usually one park open an extra hour in the morning and another open an extra three hours at night.
Whether to fly or drive is very personal. I like to drive for several reasons. I stop and visit friends along the way, and when we get to Orlando, I have relatives nearby that we often go visit. I like having my car also so I am not restricted on how many souvenirs I bring back!
Have a wonderful time!