How can the accuracy of a frequency counter be improved?

The accuracy of a frequency counter is directly tied to the precision of its timing window (the gate time), which dictates exactly how long the counter allows incoming pulses to be tallied. This window is completely controlled by the internal time base. By increasing the accuracy of the time base—such as by upgrading to a temperature-compensated crystal oscillator (TCXO), an oven-controlled crystal oscillator (OCXO), or an external GPS reference—you directly improve the accuracy of the entire instrument. While upgrading to faster digital logic improves the counter's frequency response (allowing it to measure higher frequencies without missing pulses), it does absolutely nothing to improve the measurement's accuracy.