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Red is certainly the best trainer, that's his whole character. He's the biggest idiot savant cockfighting coach in the world. His default team isn't amazing (though it gets better if you let him use later gen mechanics), but it's well balanced, and if we're going by narrative rather than ingame mechanics it doesn't matter that none of his pokemon are exactly high tier. His skill as a trainer magically lets his unevolved Pikachu stand toe to toe with pretty much anyone.
On the opposite end of the spectrum, N has a legendary and is a pokemon whisperer, but he's not really a trainer at all. He never does any training and he doesn't even own any pokemon, he just calls in his "friends" from the wild. Even after he accepts that pokemon battles are okay, he doesn't take the competitive aspect seriously. He's more interested in what battling reveals about the people and Pokemon involved than winning, so even with his jesus powers, his legendary, and his huge pool of available pokemon, I wouldn't say he's the strongest.
Cynthia is the odd one out. It's been awhile since I played DPP, but plotwise I don't recall her depicted as being any stronger than your average champion. Of course, even an average champion is strong by definition, but it's not much compared to Red's protagonist power and N's jesus plot armor. She's easily the strongest ingame though, Mt. Silver Red is a cakewalk if you put just a tiny bit of effort into teambuilding and both Black and White give you multiple options for dealing with N's legendary. She's not genuinely that difficult, but I remember having to think a little when fighting her, which by Pokemon standards makes her one of the hardest fights in the series.
Of course, this is all 100% arbitrary Goku vs. Superman-esque autism that has no real answer and we should all be embarrassed for participating in such a pointless 'conversation'. N is the strongest because Green Kaworu is my favorite :^)
