We've rented from Alamo at Disney several times, always from the Car Car Center near MK since they have the best hours. If the time works for you, there's a counter right at the Dolphin, too. It's always been pleasant and easy, with rides to and from the resort.
But, from what I remember a lot of people online said that they rented from agencies that had desks at some of the non-disney hotels in the downtown disney area. They took a disney bus to downtown disney and then walked over to the hotel.