Hard to say. You made a great case for Prophecy Girl. I agree with everything you said, but in hindsight I might go for Becomming. My opinion on this changes so often as they were all so good.
Becomming however is great in terms of how brutal and bleak it is. From Angelus' torture of Giles, to Kendra's death, to Buffy being kicked out of her school and her home and being wanted, to Xander deliberately not telling Buffy the truth, to the cruel twist of Buffy having to send Angel, rather than Angelus to hell. It was a classic piece of tv all around and absolutely shocking the first time I saw it.
Also Spike was at his best that finale. He was like an earlier Crowley, playing everyone against each other for his own benefit and then ****ing off LOL.
Even Drusilla having sadly been pushed to the side during that season got to play a big role and show how dangerous she was in killing Kendra.
Buffy's speech at the end of The Gift is the best bit of dialogue in the series however, whilst Restless is the most experimental, I agree that the metaphor in Chosen by and large is a fitting end to the show, whilst Grave might be the most touching in the last scene between Xander and Willow. Graduation Day meanwhile features the best showdown between Buffy and one of her enemies (her fight with Faith. It's even better than her showdown with the Master. As much as I like him, with Faith it's a lot more personal and nasty on both sides. "All that killing and you're afraid to die.")
Prophecy Girl meanwhile I think plays up the end of the world idea better and the Master is the best villain of all the Big Bads in his finale. He doesn't just feel like the final boss like the other big bads do in their finales. The Mayor, Adam, even Glory all just kind of felt like they were beaten too easily. (I know Glory caused her death, but even then it did feel like "hey if only we'd figured out we had all this stuff earlier we could have just killed her before" same with Adam.
The Master however isn't like that as Buffy is genuinely pushed to her limits when she fights him and loses at first. You can see why she didn't fight him before. Also beating him doesn't just feel like something they have to get out of the way. Finally his death is the most satisfying because of how much he's tormented her before hand and how scared she seemed.
They were all excellent finales.