What is the top part of a submarine called?

The raised portion of a submarine above the deck is called the Fairwater or Sail; its primary purpose is to house the Periscopes, Radio masts, Snorkel Masts, and other equipment in a streamlined enclosure. It also serves as the Bridge / Lookout station during underway surfaced operations.

In WWI/WWI submarines, the tower was known as the Conning Tower, as it was this area where the Commanding Officer would "Conn" (control) the boat during target tracking / attack situations.