There are good and not so good points to each option:
1. Disney resort express, goes first to the DLH and then to other hotels, so depending on where you are staying and where they are on the route it could take a long time. Also, you have to catch the bus on it's schedule.
2. Super Shuttle, usually a van that leaves the airport when it is filled. So sometimes you get in and it goes, sometimes it waits to fill up with people. also, it can be taking people different places and can at times be a long ride.
either way will work fine.