You need to first eliminate any options that are not compatible with your hardware and if you have enough counters for your application, you simply need to calculate the error for the expected frequency for each available option, considering the measurement time (if applicable). The best method will be the one with the lowest error at a given frequency and measurement time (if applicable).
If you want to find a numeric value for the error within each method, the Quantization Error topic from the NI-DAQmx Help shows the error at different input frequencies for the Low Frequency with 1 Counter, High Frequency with 2 Counters, Large Frequency Range with 2 Counters and Dynamic Averaging methods for a quick comparison. You can use the formulas included in the help topic or refer to the User Manual from your device for further information.
It is also possible to use multiple counter tasks if your card contains multiple counters. This can allow you to meet the needs for response time and accuracy at different frequencies.
Note: The Sample Clocked method is not included in the Quantization Error topic because it does not depend on the input frequency. If you need to compare a Sample Clocked Counter Frequency measurement with any other method, refer to the User Manual from your device to calculate the Sample Clocked method error.