Hakuba.
Searching White Horse
Here's the breakdown.
Kudo Shinichi/Edogawa Conan: As for should end up with this would be the best. They're the only two in the entire world who understand each other at that level. They challenge each other and care a ton for each other without whining about everything. Kudo has matured past his very stupid attitude that he used to have, and though Ran has been fairly mature in contrast, she's waiting for what was, not what is. Haibara and Edogawa have already fought through their differences and have both supported each other in ways no one else has. But thanks to Gosho's obnoxious childhood friend 'rule', the innocent Kudo Shinichi and Mouri Ran are almost certainly actually going to be together in the actual canon series.
Tsuburaya Mitsuhiko: ... Why?! Yes, he crushes on her. He has a bright mind for a kid his age, and when he's 18, maybe he'll be the next Kudo Shinichi, with a slightly less annoying Gary Sue (is that what it's called?) character. But Haibara Ai is actually Miyano Shiho, and would be ten years older than him. What happens when he finds out the truth? Awkward. And why should she like a child? She only does what she does to encourage him because she cares for him like her younger brother or child, even. Just like the other Shounen Tanteidan. I also don't see Haibara spilling out her life story to this kid. Ever. So, no.
Hakuba Saguru: Like I said above, this is probably best if we actually want to see her with someone. They share British descent, which is pretty neat imo. They're both extremely intelligent, and I think that they have very similar personalities, although Hakuba is much more open to people than Haibara. I think the only obstacle here is how they meet, since they have yet to do so. And there's also the problem of whether Hakuba's "Why did you do it" question gets answered and he doesn't think that the answer is acceptable. Maybe he'd react like Edogawa and say something like "How can you expect me to understand a murderer?!". But from the little I've seen of Hakuba, he's not an unjust person and I think he'd be a gentle and smart match for Haibara. 2nd best match.
Akai Shuuichi: He dated her dead sister and was the reason she was murdered. I don't think she'd ever date him. Ever. Maybe she'd come to a place of understanding (which is what it's starting to look like) but I highly doubt they'd be romantic.
There's my two cents.