Uru and Mabinogi has surprisingly good audio with theirs.

I think that "best" is open to various interpretations.

The most-emotionally-impactful in the context of the game?

The most-graphically-impressive?

The best-integrated with the game?

I often don't try and play the latest-and-greatest games, and while I'm sure that I've played games with thunderstorms in them, I can't immediately recall any recent first-person 3D games...and I've kind of shifted way from FPSes in recent years. Probably the newest 3D game that I can immediately recall playing that I distinctly recall having thunderstorms -- though I think that they were rain is modded Fallout 4; I was using one of the weather mods.

I think it was one of:

• Natural and Atmospheric Commonwealth

• True Storms

There are radstorms that impact gameplay by dosing the player with radiation, and I suppose could be considered to a different form of thunderstorm. These are separate from normal storms. Fallout 76 also has radstorms, but they are less-frequent and far-less-damaging than in (modded, don't recall base game) Fallout 4.

I guess that that'd probably be the most-graphically-impressive that I personally can recall off-the-cuff. I'm sure that there must be some newer, fancier thunderstorms out there.

For impact...I can't recall for certain whether-or-not there was actual thunder and lighting other than in cutscenes, though there's certainly rain.. But The Saboteur is an Assassin's Creed-style game (I understand; I've never played more than a very small amount of those games) set in World War II Paris. The areas that are occupied by Nazi forces are mostly black and white, with a small amount of color, mostly red, and at least some of the time, it's raining. The areas where forces have been pushed back look kind of like spring. I think that it added to the game's atmosphere a lot.

Sea of Thieves overall best. Hunt: Showdown a close second

Thunderstorms in Baldur's Gate (the old ones) could outright kill you. Scary stuff.

The opening act of Little Big Adventure 2 gets my vote.

For atmosphere, I was floored by Kingdom Come: Deliverance's storms. They really did a good job of capturing the deep rumble of an approaching storm out on the plains.

I swear I've come across an indie game that had great thunderstorms, but I can't remember what it was for the life of me.

That said, imo The Sims as a series has had good thunderstorms. Being outside can result in your Sim being hit by lightning, and iirc there are things that'll increase the chance of getting hit, like being wet, being in a pool, holding an umbrella, etc. I'm not sure which game has the best thunderstorms though.

VRchat has some worlds with really good ambience, and typically they include rain and/or thunderstorms to some extent. You don't actually need VR, you can play VRC on a normal monitor.

I've just realized that one of the things that Risk of Rain 2 is missing, is a persistent thunderstorm that gets stronger as the difficulty gets higher, lowering your visibility over time.

Mafia's "A Trip to the Country" mission has to be up there for best thunderstorm. The atmosphere in the Remake was even better.