Linearly polarised antennas propagate EM energy on a single plane: either vertical or horizontal. Conversely, circularly polarised antennas emit EM energy on two planes. Each option has a set of advantages and disadvantages, but linearly polarised antennas tend to perform best in most applications.
On the same gain, linearly polarised antennas tend to have a greater read range, this is due to their concentrated emission. So, as long as you are aware of the orientation of your device in-situ, a linearly polarised antenna would be a better choice.