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.