To expand on the above:
There is an Alamo/National counter at both the Car Car Center and the Dolphin. If you're looking to get an early start, the CCC is your better option as it opens earlier. (I think it's 6am, though the shuttle service doesn't start until 7am). Dolphin opens at 8am, though if you're at one of the Crescent Lake resorts it might be worth waiting for the convenience.
Also note that at some point the CCC shuttle stops, so if you're thinking about dropping off after-hours you might want to consider having the drop-off be at the Dolphin. Depending on how late it is you can go to Epcot or the Studios for a few hours, or it's easy enough to grab a bus to Downtown Disney or a taxi back to your hotel from the Dolphin.
If you prefer another rental company, most of the other major companies (Avis, Dollar, Budget) have a desk at one of the Hotel Plaza Blvd hotels. And most, if not all, have shuttles that can pick you up. Enterprise is nearby and will pick you up, but it's off-site and thus will require more travel time for pickup and drop-off.
-Rob