I didn't do Disney but we did Universal last year for 2 days and then a cruise. We booked our own air into Orlando, stayed at the Sierra Suites hotel for a couple of nights and then cruised out of Port Canaveral. I arranged for private transportation through Legacy Limo service. It worked out fine. I have taken my kids to Disney before without a cruise. Again I've booked it myself as I found I could do it cheaper. Both times we went we stayed on property at one of the all star resorts. If your kids are young this is the way to go. We would go to the parks early, back to the room between 2-3 p.m. for a swim, nap, dinner, etc. and then go back to the parks at night. The All Star resorts have food courts that are pretty reaonable. I think when we were there 2 years ago a chicken fingers and fries dinner for the kids was $3.99. I would do Disney first and then the cruise. Much more relaxing that way. If you live near a disney store you can buy your park tickets there and then not have to wait in line when you get there. If your kids are 6 or less I would rent a stroller for the day. I found that my 6 y.o. got tired from all the walking and then was cranky. Once we got the stroller it was much better. It also gave us a place to put all of our stuff!
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