What was Geralt's third wish?

The answer was neither in the book nor in the show yet, from screenrant

In Sapkowski's written version of "The Last Wish" Yennefer addresses the wish immediately after they are spared death from a crumbling ceiling (a home in the Netflix series, a tavern in the book). Saying "I heard what you wished for" and that Geralt's decision "astounded" her, it's a major part of what sparks their session of lovemaking. When they finish, Yennefer revisits the scale of his wish... and what it may cost him:

'Your wish,' she whispered, her lips very near his ear. 'I don't know whether such a wish can ever be fulfilled. I don't know whether there's such a Force in nature that could fulfill such a wish. But if there is, then you've condemned yourself. Condemned yourself to me.'

The Netflix version can't communicate Geralt's words loud enough for Yennefer to hear without the viewers also knowing, which is important. The books themselves never explicitly confirm the truth shared by Geralt and Yennefer, but they do explain the problem more than the show does. With Geralt's life in danger along with Yennefer's, a wish can only be used to save one of them. Unless Geralt gets clever.

But for the show:

Which is when the priest drops the closest thing to an explanation fans may get, saying:

"It's not that simple... But if... If he expressed the right wish... If he somehow tied his fate to the fate... No, I don't think it would occur to him. And it's probably better that it doesn't."

Most fo speculation is he tied their fate or asked for the kid with her etc as said in another answer.

For the word of god from TV Guide

"We know," she confirmed. "I'm not sure anyone else will ever know. But to know the story, we had to very much decide on, 'This is what we're hearing,' so that we can make sure that as the dominoes fall in later seasons we all understand what it is."

When asked whether the audience would find out what Geralt wished for, Hissrich played coy, saying that she likes "to let the audience keep guessing on that one" for the moment. However, Anya Chalotra is confident that the series will reveal what Geralt wished for... eventually. "Absolutely. Yeah. I'm sure," she said.

So we should be patient and see.

SPOILERS AHEAD!!!

Even in the books it's a mystery. Andrzej Sapkowski (writer of the Netflix series) pointed out that eventually the third wish will be revealed during future episodes. What's for sure is that whatever Geralt has wished for is a wish that could save Yennefer's life. Therefore, two main theories are considered:

1. Geralt wished to have a child with Yennefer, since that would prevent the djinn from killing her in that moment and would bind their lives together through this fate and their future child.

2. Geralt wished to die alongside Yennefer. Since a djinn can't kill its own master, this wish would provide a nice loophole that would save Yennefer's life and also ensure that Geralt and Yennefer's lives are bound together until their very ends.

Here's the source and further details of what was said above

In S01E06 Rare Species, Borch Three Jackdaws gives us this insight into the nature of Geralt's wish:

Borch: I can see why Geralt didn't want to lose you.

Yen: What does that mean?

Geralt: In Rinde. The djinn.

Yen: That's why we can't escape each other. Why I feel this way inside.

Geralt: No.

Yen: It's not because of anything real or true. You made a wish. It's magic.

Geralt: It's real, Yen.

Yen: How could we ever know? Disregard for other's freedom has become quite your trademark.

Geralt: I made that wish to save your life.

Combined with the dialogue from Bottled Appetites:

Geralt: My plan worked.

Yen: There was no plan. You were making it up as you went along. Any fool could see. What did you wish for? Tell me.

If you allow the cannoninity of the games, in Witcher 3, Wild Hunt, there's a side quest where Geralt and Yen go catch another genie and use the wish to undo the first wish. This is seen in the quest, titled appropriately enough, "The Last Wish". From the journal entry added after quest completion

Together witcher and sorceress managed to pin this feisty spirit. Once it understood its situation was hopeless, Yennefer could convince it to do what she wanted - release Geralt and her from the spell another djinn had cast on them long ago. This spell had made it so that Geralt and Yennefer, despite their many differences, could not live without each other. Now they had a chance to see if, once the spell was no longer in effect, the magic between them would still persist...

https://witcher.fandom.com/wiki/The_Last_Wish_(quest)