Hmm, I never weighed in on this . . . though I haven't played the last few games, I could perhaps add something.
In terms of raw physical power, I'm pretty sure it's Suika.
In terms of raw magical power, I'm not sure, but I expect that the likes of Flandre, the Wataskuki sisters, Ran, Kanako and Suwako, Yuuka, maybe Marisa, and from the sound of things, Hecatia, would be in the running. (also Mima and Shinki, if you're willing to count them)
For "game breaker" type powers, there's of course Yukari, Sakuya, Remilia*, Mokou, and especially Yuyuko.**
Finally, there's just plain skill, which I would put all of the main playable characters as being high on list, given that the games, by their nature, suggest that these characters are capable of turning the tables on more powerful foes through skill. Which of course, would suggest that Reimu is the best fighter in Gensokyo by pure skill.
Trying to factor all of this together would a nightmare, but I actually think that altogether we would have chiefly the Watasuki sisters, Yukari, and Yuyuko. The sisters have rediculous amounts of magic power and pretty much cheat, the latter two have a lot of power, complete breakers of abilities, and are exceedingly clever (it's shown with Yukari, but really only implied with Yuyuko). But even then, there's so many unanswered questions about characters' powers and they may or may not work, that it could honestly just depend on how someone writes it out.
Hecatia is a mystery to me, not just because I haven't played the game she's from, but because I'm not sure how she fits with setting. The other gods we've seen were Shinto gods (I think) who lacked power due to faith, but were still very powerful. Hecatia is based on a Greek goddess though, so I don't know how she would fit. On the other hand, being based on the Greek goddess of black magic, it would actually make sense if she automatically was just better at magic than anyone else . . .
Since Satori was brought up, I think it bears mentioning that while Satori's mind-reading gives her an edge in skill and cunning, she doesn't seem to have the excessive power that the upper levels of the characters have. She might be able to win against some people somewhat more powerful than her thanks to it, but if she doesn't have the power to actually counter the things her opponents will do, then knowing what they will do isn't going to do her much good.
*Remilia's manipulation of fate is really sketchy. It doesn't seem to be a power she actually uses, and it doesn't really seem to do much. Personally (headcanon), I think the ability isn't anything more than her odd way of getting off scott-free when she messes up, or messes with the wrong person. Otherwise, I'm just not sure what it actually does.
**Yuyuko is a strange case. The idea that she can just will someone to die if things get serious is crazy enough, but since we've never seen it in action, we don't know if it has restriction (i.e. does it work on gods?). There's also that she's not only already dead, but queen of the Netherworld, which probably grants her some protection that normal ghosts wouldn't have. She probably couldn't be . . . destroyed by most opponents. Maybe she can't be destroyed at all, or only a higher authority like the Yama*** could end her.
***Speaking of the Yama, I'm not sure where she falls. Komachi is expressly stated to be powerful, but beatable, but I seem to recall the Yama being implied to be unbeatable by virtue of her job. Not sure if I'm remembering incorrectly, or if there was more to it . . .