Risk of electric shock

The mere fact that you find water inside an underground conduit is nothing, all by itself.

The NEC defines "Underground" as a wet area. Normally there are weeping holes in the conduit to drain water out of the conduit.

Now that said, what are you not telling us? For example, was this conduit damaged by Sandy and severely ruptured?

Without more information I would treat this situation with the upmost care. I would make sure that all power is cut off for the conductors inside the conduit and then start checking for faults between the conductors and the conduit.

I've never know conduit to have weep holes. They would let the water in as much as let it out.

It is almost expected that an underground conduit will fill with at least some water. This is not a problem.