According to Netheril: Empire of Magic (N:EoM), at the time of the Netherese there were very few human deities and each one of them carried very many portfolios. It seems like as the millennia went by, those portfolios got shared by many new powers.
For Mystryl, the list went like this: Magic, spells, the weave, wizards, spellcasters, energy, creativity, knowledge, invention, song, time, spring (page 49 of The Winds of Netheril).
We can compare this list with the portfolios given in the FR Adventures (FRA) and Faiths & Avatars (F&A) sourcebooks. We see that every portfolio except Time is covered: Azuth (mages, energy according to FRA; wizards, spellcasters according to F&A), Oghma (knowledge according to FRA; knowledge, invention according to F&A), Lathander (spring according to FRA; spring, creativity according to F&A), Milil (song), and of course Mystra (magic, spells, the weave).
Given that every other one is somehow covered, and the great many commonalities between N:EoM and F&A, I would agree with Carcer's statement and say Time appears to have been intentionally left out by TSR. (F&A lists Julia Martin with Eric Boyd as designers. For N:EoM, Julia Martin is listed under "additional design" and Eric Boyd is listed as a proofreader.)
There is one final curiosity: Amaunator is mentioned (in both N:EoM and F&A) to have misinterpreted some godly contract and wanted to preside over passage of time, but decided not to interfere with Mystryl. It looks like after Mystryl's demise, he still did not claim Time. So perhaps Mystra could still be the "hidden inheritor" of the portfolio and might someday claim it openly. It might also be worth mentioning that three "time gates" that allow characters to travel back to the Netherese period were still active as of 1370DR, and they were being protected by Mystryl's magic (N:EoM). It would be an interesting scenario to have Midnight/Mystra sending an avatar/proxy to meet her old self, Mystryl.
On a related note: Here is a list of powers from F&A who grant major access to the sphere of Time to her/his speciality priests: Amaunator, Auril, Chauntea, Cyric, Eldath, Kelemvor, Leira, Mask, Mielikki, Myrkul, Mystra, Shar, Silvanus, Sune. We broadly see that they are mostly deities of nature, death, or deception. If you really want to assign the portfolio of Time in your own game, consider one of these.
Deities followed by chronomancers
There is an article with the title Chronomancy & the Multiverse, version 1.1 by Roger E. Moore, published as "an updated and expanded excerpt from the Chronomancer", a 2e accessory. The article was made public by the WotC on their free downloads for previous editions site. This article has a section of the effects of chronomancy in the Realms, and relates time with deities of knowledge and writing. It is stated:
Native chronomancers are usually devout followers of both a deity of magic (e.g., Mystra) and a deity of time or history (e.g., Deneir or Oghma), serving as historians and information collectors. Elven chronomancers of Labelas Enoreth are possible. Shou Lung, in Kara-Tur, might have a secret, officially approved group of chronomancers, probably Historians, working for the Emperor.
I think the Arcane Age and Karsus's Fall entered canon sometime around 1995-1996.
Karsus was described as a "lesser-known" deity in a half-page article by Eric Boyd published in the February 1995 issue (#104) of the Polyhedron magazine. At this point, Karsus is not a dead power and his demise (from greater deity to demigod) was attributed to his poisoning by a Netherese mage named Wulgreth, who sought to steal immortality from Karsus (ironic, isn't it?). So we can conclude that early 1995, Karsus's story as we know it was not yet canon.
TSR released the Netheril: Empire of Magic (N:EoM) boxed set in November 1996. Yet we can argue that Netheril storyline was already entering the FR canon before N:EoM's publication based on evidence from the sourcebook Faiths and Avatars (F&A), which was published in March of that year. F&A has plenty of information about Mystra that foretells the then-upcoming Arcane Age storyline: Mystryl is given as one of Mystra's aliases; her speciality priests can also be of the CN alignment (Mystrl was CN); one of Mystra's symbols is none other than Mystrl's symbol, a single blue-white star. It is worth noting that one of the authors of F&A was Eric Boyd.
Powers and Pantheons (P&P), a companion to and continuation of F&A, was published in 1997. At this point it is clear that the whole Karsus story is canon: P&P lists Karsus as a dead demigod, describing explicitly the events in the earlier Netheril material; including his 12th level spell, and how he used it to steal Mystrl's power and ended up dead.
1998 saw the expansion of the Arcane Age material further with the publication of Cormanthyr: Empire of Elves. This product is also in full support of the Karsus's Fall story, including all the events in the earlier Arcane Age material.
The conclusion is that Karsus's Fall became canon during the 2e of AD&D.
Best Answer
The AD&D 2e boxed set Netheril: Empire of Magic provides a whole list of major NPCs that played a significant role in the 3500 years of Netherese history. Unfortunately none of the arcanists listed under the Silver Age were alive in 1101 NY (−2758 DR). Terraseer (one of the oldest beings on Toril, also known as Arthindol), Congenio Ioun (considered the first great arcanist of Netheril, inventor of ioun stones), Ioulaum (inventor of the mythallar) were around, but it is not clear whether they were amongst the members of the council named the High Mages of Netheril.
However, we know that in 1048 NY, the number of floating cities/enclaves was already 13 (page 7 of the Winds of Netheril from the boxed set). One of them had been raised by Iolaum, and he was the ruler of his city, Xinlenal. Given that the top arcanists are said to have formed the High Mages of Netheril, it is natural to assume that these included whoever raised those enclaves into air.
Another good resource to look for candidate members is the 3e book Lost Empires of Faerûn. A blog by Xaeyruudh gives a list of all the fifty something enclaves along with citations including page numbers. Unfortunately, only Xinlenal dates back to before 1101 NY. The earliest other enclaves we have data on are Akintaer (established by an unknown arcanist in 1173 NY), Palter (established by arcanist Halavar in 1217 NY), and Orbedal (established in 1247 NY, arcanist not listed).
The one person we are sure to have been one of the High Mages of Netheril is Lady Saharel, mentioned by Elminster in the novel Shadows of Doom and later in the 3e campaign adventure Anauroch: The Empire of the Shade (page 90). Her position as a political leader was confirmed in posts from January 2018 on the Candlekeep forums. However it is not clear which age Lady Saharel lived, so it is unclear if she was one of the High Mages in 1101 NY.