Two grayish shapes steered there, like long, rounded pieces of wood or slate. They were fish. He saw them nose toward each other, poise motionless, make a dart forward, swerve off, and come around again. It was like a water dance.

In this first quotation, there are two similes describing the movement of the fish. The first simile compares the fish to "pieces of wood or slate," suggesting that at first they might appear to be merely pieces of driftwood or slabs of slate. This simile helps us to understand how startling it must have first been to see them move and "dart forward." In the second simile, the movement of the fish is described as "like a water dance." This simile emphasizes their gracefulness and harmony. Their swimming seems perfectly coordinated, like a dance.

A few inches above them the water sparkled as if sequins were dropping through it. Fish again—myriads of minute fish.

In this second quotation, the movement of the fish is compared to sparkling "sequins" dropping into or falling through the water. This simile highlights how small the fish are, and the imagery connoted by words like "sparkled" and "sequins" also suggests that the movement of the fish is beautiful and precious.

There are several comparisons in "Through the Tunnel" about fish.  Some of the similes are about the fish, and the other similes are about Jerry being like a fish.  

The first simile is after Jerry gets his goggles.  He can see underwater really well, so he is impressed with all of the beautiful fish that he sees.  During that time, the following simile is used.  

Two grayish shapes steered there, like long, rounded pieces of wood or slate. They were fish.

In that same paragraph a bit later, Jerry sees a bunch of silver colored fish swimming around him.  He describes it with a wonderful simile.  

It was like swimming in flaked silver.

The next two fish similes are about Jerry being similar to a fish in some way.  They both occur near the end of the story after he has made his lengthy swim through the tunnel.  The first is when he surfaces for air.  

He was gasping like a fish.

Then at the very end of the story, Jerry's mother is asking him a few questions about his day.  She is a little worried about his injured head, but then she dismisses the worry because she knows that Jerry is a great swimmer.  

Nothing can happen. He can swim like a fish.