This topic was discussed not too long ago, but I can't find the thread offhand either here or on Tweak City, so I don't know.
Either way, I own a pair of O-3's (which are omni-directional, but not dissimilar to the N3's) and I own a set of Ninja modded Mini's w/ Sonicap Platinum bypass caps. So, I can at least take a stab at this one. IMO, the stock Mini is solidly beaten by the N3's. Fortunately, you can get the Mini's to sound much better if you do the Ninja master upgrade. With the Ninja mods, the Minis are crisper and image better than the stock version and are overall well worth the money. Now, does that mean that the Ninja'ed Mini's are on par w/ the N3's (or O-3's in my case)? Not really. The Neo based drivers are really something, and unless you really dig the intimate sound of the Mini's, then the N3's are likely better. However, when Sonicap Platinum bypass caps are added to both, then, to me at least, they likely become a lot closer in overall quality. The Platinums helped the O-3's, but when I added them to the Mini's, there was a significant (and surprising) level of improvement. With the Platinums, the Mini's no longer get beaten solidly, and to me, it becomes a toss up as to which speaker is better. The Mini's are lovely for intimate listening, and the O-3's are grand in their sense of space. So, a matter of opinion more than anything else.
So, a couple of other things. The Ninja mods, especially if you add Sonicap Platinums, are not cheap, and alone can run close to the cost of the N3's. Also, you have to consider the woodworking. If you can't do work work, like myself, but can handle a soldering iron, then the Ninja mods for the Mini's are perhaps a better choice.