The Cambridge Dictionary provides different definitions of waking as a noun and as an adjective. The noun meaning relates to the moment of waking. In this context, the word is used as an adjective, and so the adjectival definition is relevant: used to refer to a period of time or an experience during which you are awake.
According to this definition, waking means marked by full consciousness, awareness, and alertness. To quote further from the link:
This adjective most often occurs in phrases such as “every waking moment", “every waking hour", “every waking breath", and so on, the sense being roughly “at all times". Such phrases are often used together with possessives, such as in “her every waking moment" or “my every waking thought".
So, waking thoughts refers to anything that you think about when you are not asleep.
The expression can be used to describe what you are always thinking about: this might be relevant in this context, but it is more likely to simply be a contrast with the reference earlier in the paragraph to in his dreams.