This is a vexed question.
People usually won't hear a difference of three cents or less, so that's a sort of acceptable first target: if you can get it that close it's 'good'. But there are complications.
Precision has to be in reference to some standard. Since guitars are usually set up in 12-tone Equal Temperament that's the usual reference. As with any temperament it's a compromise: there are no 'pure' beatless intervals except for the octave, and some intervals are very far from 'pure'. Major thirds are off by 14 cents, iirc. For the most part you get used to the issues, but the further from 'pure' the intervals are the harder the problems are to ignore. If you add a three cent deviation to the 'normal' fourteen cent out-of-tuneness of the third it's certainly likely to be grating.
There are various tuning schemes that will 'sweeten up' the usual guitar keys. Of course, you pay for that in that the less-used keys sound worse. Equal temperament became popular because it allows for free modulation from one key to the next without a change in affect; each major or minor key is 'out' in the same way as every other. It's also the only temperament where all the semitones are equal in size, which means that you can use straight frets. 'Wiggly' frets are another way to get 'better' intonation at the cost of free modulation. There have been several threads on all of this recently.
Most intonation issues these days are caused by changes in string tension when you fret notes. You very seldom see misplaced frets on newer guitars, as you sometimes did in the old days. One of the problems here is that 'nylon', like 'wood', is a class of materials. Just as oak and rosewood and spruce differ from each other, the various types of nylon do too. Each string maker chooses a nylon that gives them the sound they like, and one brand of string can stretch very differently from another.
It's become more common in the last fifteen or twenty years to 'compensate' nylon strung guitars by moving the bridge saddle to take the stretch and tension change of the strings into account and correct the intonation. More recently luthiers are also shifting the nut for the same reason. Each different brand and type of string can require different adjustments, which should also take things like the action height into account. This is not something that a manufacturer can do, since they don't know in advance what strings and action a particular guitar will end up with. Properly done this can usually get you to well within the 3-cent guideline.
A secondary source of intonation errors is the vibration of the top of the guitar itself. If this reaches a relatively high amplitude at or very near a played pitch, or an overtone of one, it can cause intonation errors. Usually this is more common on 'better' guitars, since what makes them better, in part, is that they tend to vibrate more easily. This will alter the pitch of specific notes, and, again, it can't be predicted, only measured in the final product. Some makers will fine tune the compensation of the nut and saddle to achieve a compromise that minimizes the problems.
As you can see, that word 'compromise' comes up a lot. If it's any consolation, a well set up guitar with a good set of new strings can be about as close to 'perfect' in intonation as it's possible to get except in electronic instruments. This will be far better than, say, the average piano.