Who are Nick Fury and Maria Hill working for?

Now we do have a partial official answer from Captain Marvel Prelude:

Fury and Hill aren't working as part of a new spy agency at all, and they're not field agents for a new big-screen version of S.H.I.E.L.D.. Instead, they're operating independently, drawing upon resources Fury had presumably hidden away while he was director of S.H.I.E.L.D.. It shouldn't really come as a surprise, as Nick observed in Captain America: The Winter Soldier, "If you wanna stay ahead of me... you need to keep both eyes open." Fury is a man whose secrets have secrets, and he'd evidently prepared for the day he would need to step back into the shadows. It seems he only stepped back into the light to make an unsuccessful attempt to get the Avengers back together.

It looks as though Fury retained a wide network of allies; there's a reference to Klein, a S.H.I.E.L.D. loyalist seen in both Captain America: The Winter Soldier and Avengers: Age of Ultron. According to Fury, Klein works for a company known as Transpo, and they're ideally suited to helping cover his tracks. Meanwhile, a later scene in the comic sees Fury toss out a throwaway reference to Colonel Rhodes, clearly implying he was still in touch with War Machine. It's unclear who "Control" was, but it could be a reference to either Klein or even the Avengers Compound staff. - screenrant

The most consise answer to your question would be:

No.

There has been no confirmation, either in-universe or out of it, as of today, that would tell us who Nick Fury was talking to at the end.

But, there are several theories as to what that might be. Keep in mind that they might not be working for someone, but with someone, or even just have a direct line to someone that Fury would like to call at this point, without necessarily working together.

1: The Guest House organisation:

In Agents of S.H.I.E.L.D., when Coulson and Garett infiltrate the Guest House, they find people there who were not shield agents. Yet, they had obviously worked with Nick Fury to save Coulson after his death. They were pretty well organised, obviously extremely well funded, and ready to die for their cause, bringing down the entire facility, if anyone were to breach it. Those two guards were definitely not the creators, and the question remains, who created and funded the Guest House, and what other secrets do they have?

Nick definitely had some way of contacting this organisation/person, since he did it the first time, so "call control, code red" might be a reference to that. It doesn't mean that they work for this entity, just that they have a number, maybe only for emergencies.

2: Captain Marvel

Just because Nick contacted her without mentioning any "control" or "code red" again, doesn't mean that the original order he gave to Hill wasn't the exact same thing he did himself a few seconds later. The device to call her was very accessible to anyone (but maybe required fingerprints or something to actually work). So maybe nick told Hill to call Captain Marvel or her team (called "control"?), then seeing her vanish he decided to run do it himself instead.

3: The Avengers / Secret Avengers

Nick Fury doesn't seem to have had any interactions whatsoever with the Avengers during the movie. Except for New York, all the Attacks were not very public. Right at the beginning of the scene, they mention having no news from Stark, so it would seem that they saw Stark "taking care" of the New York invaders and leaving in their ship, and have been waiting for an update since then, maybe getting increasingly worried after getting word of Europe or Wakanda's attacks.

You could imagine Fury, having some way of contacting all the Avengers including the exiled one, deciding that Code Red means they are all needed right now.

4: The Government

Not only did Fury probably reveal that he is alive to someone with power somewhere, to get ressources and maybe fake IDs, but anyway Maria Hill is alive and well to the public. Either one of them could have an emergency line to the army, the UN, or just the government, and the ability to send a few emergency codes, including the red one. Maria Hill worked with the US army at the end of the first season of agents of shield, so it's not out of character.

5: Other superheroes

The original Avengers initiative was a secret project, that was scrapped, then revived when Loki attacked. Shield has been aware of superpowered people for decades (Agent Carter), and even though there are very few of them (the index is a short list), the inhumans multiplied during the last few years after season 2 of agents of shield. It would not be surprising for other Avengers initiatives to have existed, either with shield or as a project of Fury after faking his death. The events of Civil War would be a good motivator to convince him to have a plan B. It's not like the Marvel Universe doesn't have dozens of other superheroes to choose from, including most heroes from the TV shows. Maybe Fury is just calling in "backup Avengers" since something is going South and Stark is nowhere to be found.

6: Villains

Shield has been locking away superpowered villains for decades, and not all of them got out when Hydra attacked. You could imagine a Suicide Squad-like scenario, where Fury has been keeping tabs on captured villains for a while even after his fake death, putting together a very last resort team. The Avengers are there to fight the battles they never could, and the Badvengers are there to fight the battles they never would. Specifically, Emil Blonsky (Abomination) would be a possible candidate, and there are probably many like him that had their stories off-screen.