There are a number of key players in the book who could be candidates for "Heir to the Empire":
1. Grand Admiral Thrawn
Thrawn was the only non-human to be granted the rank of Grand Admiral in a secret ceremony years before. He is an excellent tactician and was highly successful at shoring up the remains of the old Empire
2. Mara Jade
She was the Emperor's Hand, a secret Force-sensitive operative who directly did the Emperor's bidding. While she believed she was the only Hand, Grand Admiral Thrawn hinted at the existence of others.
3. Luke Skywalker
Luke is the son of Darth Vader, who was being seduced to become the new apprentice of Darth Sidious (aka Emperor Palpatine) at the expense of his father. Ultimately though, he (and indeed everyone else) was being manipulated by:
4. Joruus C'Boath
Note that "uu" in his name. He was the clone of the Jedi Master Jorus C'Boath, who was lost as part of the Republic's venture to explore beyond the galaxy. Joruus C'Boath is quite insane, perhaps as a result of cloning a Force-sensitive mind. While he was originally a tool for Grand Admiral Thrawn, ultimately he had his own agenda and tried to bend both Luke to become his servant, even to the point of creating a clone of Luke (Luuke Skywalker) from the hand he lost in Bespin.
So who is the "Heir"?
In reality, it is Joruus C'Boath, not Grand Admiral Thrawn. He fell to the Dark Side in his madness, and began to style himself as a new Galactic Emperor. With his power in the Force and his Dark side, he was the the one most likely to succeed Palpatine as Emperor.