It is the nickname for Ford manual transmissions built in the 60's-70's that have a case where the guts are installed/removed/repaired by removing the top cover plate.
The new 5 speeds have a top plate too, they are not known as "toploaders"

 

It can be both 3 speed & 4 speed. All it means is that the gears are accessible from a plate on the top of the trans. Most people seems to want them. They are good transmissions.

 

Toploader 4 speeds seem to be strongly desired. From what I understand, they are a strong transmission and obviously last for years! I have a toploader now, but may do the T-5 conversion one of these days.

 

As stated, plate on the top, all gears load from top. This is in contrast to the Borg Warner transmissions also in the Mustangs that had a side plate, and gears came in from the side, but are not as strong, and harder to get parts for. There was the 2.77 (6 cyl 3 speed) with 4 bolts on top, piece of junk, the 3.03 3 speed, forget how many, about 12 bolts on top, typically had an aluminum tail shaft, then the toploader 4 speed. They had an iron case, iron tail shaft cover, and had 3 "bumps" on the side where the shifter prawls attach. They made about 135 different TL 4 speed trans, including different tail shaft lengths, different input splines, output splines, gear ratios and case fronts (mate up to different engines). Beware of the SROD (Single rail overdrive) transmission, which looks like a toploader. Has a later model casting number (Believe D4 and up ??) that is often mistaken for a toploader.

 

they must be ok as i had one (3 speed) (still have the tranny) in a 66 pontiac. and yes it came from the factory that way.