It depends on the RTC device.
If it has the feature of a clock output as most do, divided down from the main crystal, the easiest solution is to compare it with an accurate frequency source and work out the calibration value based on the difference. For example, if it has a clock/4 output at 8192Hz, read that frequency and derive the correction factor from it. I would not advise connecting to the crystal directly as your probe will shift the frequency slightly. I did it once using a microphone and accurate frequency counter, the microphone could hear the vibration inside the crystal so no electrical connection was necessary!
Brian.