I have question for you since you seem to know about the clocks. When the manufacturers say accuracy is 3ns/day, does it mean that they are talking about the receiver accuracy, the receiver can keep time within 3ns? we know that the GPS signal can never give that accuracy? Are there two different types of accuracy, GPS signal has an accuracy and the receiver has its own accuracy which could be better than the GPS signal.
3ns/day means the clock can drift by 3ns a day. But this would be a pretty good clock (better than Rubidium IIRC)
Over a long term (> week) time from GPS is accurate. Short term (<48 hours) it will drift about +/-50ns. So if you want to have stable (I'll get to accurate later on) time from a GPS receiver you will need to have a local oscillator (OCXO, Rubidium or Cesium) that is corrected slowly using the GPS time. With a Cesium clock you can achieve good stability by doing a tiny amount of trimming (= averaging the GPS time); so little that the Cesium is basically freerunning. OCXO and Rubidium will drift much quicker and require more adjustments so the time is not that stable.
Where it comes to accuracy: you'll need to calibrate the cables for the GPS receiver to take their time delays into account but also think about the internal delays up to the point where you need to use the time (for timestamping for example).
The GPS time is sourced from the USNO (US Navy Observatory) by using a whole bunch of Cesium clocks. And typically this time source is also compared with many other institutes who have their own clocks. There are lists available that tell you how much GPS time was off so you can correct timestamps afterwards as well.
However, the use of NTP suggests you are looking for a clock source that stays on track over a long period. For that a GPS receiver will do just fine. Likely the NTP server will have an OCXO internally to keep track of the GPS time and keep going during a GPS outage / breakage. That is also where the 15ns/day number is coming from: the internal oscillator (likely Rubidium) can drift that much when it is not corrected from the GPS time.