Due to the number of stops and the order in which the buses travel, it can be a frequent occurrence to have guests on the bus when it arrives at your stop.
Unfortunately, there is no fast and easy formula to assure yourself of an empty bus.
All of the buses have 2 tie down positions. Some of the new Gillig's have three and the 10 new Nova's all have three spots. One bus, 4815 has four tie down spots and can be arranged by a call to Disney Transport (Be aware that there may be a long wait as this bus is in regular service and may not be available right away)
Riverside:
For MK and DTD, the best stop to get an empty bus will be the West Depot. If you are going to these parks, avoid the South depot if you can as this is the last stop and you will be guaranteed guests on board at almost all times.
For EC and DHS, the best stop is actually French Quarter as those buses stop there first, then proceed to the South Depot.