Shr'akt'lor has a population of about 2,000,000. Typical githzerai cities are said to have a population of 100,000 or more. In 1e they were said to only have 100-600, so it looks like population inflated 100,000% between editions. Going by the 1e times one thousand rule, githzerai cities typically number 100,000-600,000, which fits very well.
The population of the Floating City was never defined in Planescape. In 1e it only had 10,000 (not counting non-githzerai), which comes out to 10,000,000 in Planescape numbers: way too much. Make it 1,000,000, half that of Shr'akt'lor but still very big for a githzerai city, as befits its spiritual capital.
Toroj has a population of 850,000, and claims to be the githzerai's second-largest city. It's actually probably its third-largest, since Orri forgot to count the Floating City. That is, unless we decide to shrink the Floating City down to 100,000 and make it a place only elite sorcerers and rogues visit.
What Planescape called githzerai fortresses are apparently the same as their monasteries in 3e. These usually have about 3000 githzerai in them, which seems large, but I'm not aware of anything that contradicts this figure. Make it 1000 to 6000, so they're one-hundredth the scale of 2e githzerai cities.
Githzerai monasteries on the Material Plane typically have about 500 githzerai. Make it 100-600 for symmetry's sake.
According to the Planar Handbook, Tu'narath's population is only 100,000, making it tiny compared to the githzerai capitals. A Guide to the Astral Plane said Tu'narath had "over 10,000," which is pretty amazingly small. It didn't specify that of the metropolis of Githmir, but it says the "populated" cities of T'n'ekris and Xanvadi'm have about 8000 githyanki each, less than a hundredth of what their githzerai equivalents would have. The Planescape MC says that a typical githyanki stronghold has up to 1000 githyanki, plus 20-80 knights. That's only about a third of what the same book says githzerai fortresses have, and the same as what the 1e MotP said (apparently outside Tu'narath the githyanki haven't increased in population at all between editions).
Githyanki lairs on the Prime have only about 30-60 githyanki in them, apparently not counting any children.
Why is it, do you think, that githyanki are so thinly populated compared to githzerai? Is it because they're reluctant to leave the Astral Plane to reproduce? For many, reentering Time can mean instant aging or death, so this is a reasonable explanation. They have magic that lets them leave for short periods of time without harm, but it might be stretching things to wait around for their eggs to incubate and their children to grow to adulthood. Perhaps the githyanki feel they don't have enough people to spare for such a task. It's also possible that the more agressive githyanki die more often in battle, especially with psurlons and other Astral hazards to watch out for. Finally, it might well be easier for anarchs to shape large cities (they can sustain them unconsciously) than it is for githyanki mlar to create communities from ectoplasm and nothingness. Githyanki communities might be limited by the sizes of the dead gods they're built on, while githzerai communities are limited only by the imagination of the anarchs.