Joe,
As far as code references, you start with 250.20(B) which will require the secondary of your transformer to be a grounded system, at least for any of the commonly used voltages. Then to 250.30(A)(1) that will require a system bonding conductor to bond the secondary grounded conductor to the equipment grounding conductors. 250.110 will require the exposed metal parts to be connected to the EGC. This results in the primary and secondary EGCs both connected to the transformer case. Under the NEC it is really impossible to have a electrically isolated system with some rare exceptions.
In addition the voltage in this case most likely has nothing to do with the power service to the dock. It is most likely stray voltage from utility primary grounded conductor current flowing in the earth/water.
Don
