Flying. I make this trip several times a year, so I am speaking from experience. 99% of the time I take flights on JetBlue or Delta from JFK to MCO - sometimes from LGA.
When flying, from Manhattan, it's an hour to the airport, an hour for TSA and being at the gate the suggested 30 minutes prior to boarding. The flight is an average of 2.5 hours, and then factor in how long it takes to get to your destination in the Orlando area - can't be more than 30 minutes anywhere (Disney, Convention Center, I-Drive). So from NYC to Orlando via air, you're looking at a time commitment of 5 hours. Flights to Florida are in the neighborhood of $300 - add on to this any meals, transportation to the airport, cost of a rental car on the Orlando end if needed, which are typically about $20/day in Florida - say $450.
I recently drove my parents' dog from Manhattan to a town in Central Florida that is 62 miles SE of Orlando. I left at 5 am and arrived at my destination 16 hours later. Expect the same if you drive with as few stops as possible - I did have to stop every 3-5 hours for both me and the dog: quick meals, bathroom breaks, re-fueling - you can definitely make it in a day, and with the low cost of snacks and water for the car, fast food meals and fuel.
Flying is the way to go. You're looking at a time commitment of 5 hours and a cost of $450. Even if you love driving like I do - it is not a great experience. Spending 2.5 hours on a cramped plane is better than 16 hours in a car. Driving is less expensive, but it takes 3x the time to make the trip.
You don't indicate if you are traveling with others, and if you are more concerned with saving time or money. Either way - fly.