By and large, RF (particularly RFID) simply won't work underwater, particularly at the depths associated with crab pots. RF attenuation of seawater is just too great. Note figure 7 of the paper. At 1 MHz, attenuation is ~40dB/m, and pots at 100 meters down simply aren't going to hear a transmitter of any reasonable power, much less retransmit their IDs. Going to longer wavelengths helps, but not a whole lot.
Nuclear subs managed to listen for radio signals while submerged, but they used extremely low frequencies, long (100 meter) antennas, and bit rates in the vicinity of 1 bit/second. Not exactly useful for your application.