By percentage...well, no. That would actually be his current head coach, Steve Kerr (45.4%), but for what it's worth, Stephen Curry does rank third (44.1%). But three times, Curry has also made more three-pointers in a single season than Kerr ever
attempted in one year. Those three marks all rank in the top five for threes made in a single season: 286 (2015, 1st), 272 (2013, 2nd), and 261 (2014, 5th). He's made more three-pointers through his first six seasons than anyone else in history, and despite the volume of threes he's taken and the amount of attention he receives defensively, he's done it at the third best clip of all-time.
He currently ranks 50th all-time in career three-pointers made, and if he knocks them down next season like he has these past three, he'll be moving up several spots on the list. In fact, if he tops 186 threes made next season, and the four active players immediately ahead of him on the all-time chart - LeBron James, Hedo Turkoglu, Manu Ginobili, and Mike Dunleavy - make the same number of threes (or less) next season as they did this season, he'll move ahead of them. 264 made threes - a mark he's topped twice in the past three seasons - will also take him from 50th all-time to 25th all-time, in the span of one year.
The stats speak for themselves, but watch the guy play, and it's clear that he can flat out shoot. He makes it look effortless, whether he's open or closely guarded. Take away the defense entirely, and he'll knock down
77 consecutive threes in practice, and a total of 94 out of 100. Anecdotal evidence describes it well, stats back it up. He's a surgeon from beyond the arc.
At this point, I would have to say that he is indeed the best three-point shooter in history. Granted, if players like Larry Bird had played with a three-point line in college, or players like Jerry West had a three-point line during their NBA careers, the record books might look very different. But what-ifs don't detract from what Curry has done, and we can only evaluate him against the records that actually exist, in the era that the three-point line has actually been used in the NBA.