I don't think so. "Good idea" can often refer to something which just pops into our heads, like an inspiration.
"Good thinking!" logically suggests that the cognitive process might have been used. That is, we reason things out and make a suggestion based on careful analysis. But both expressions imply concurrence. You like and agree with the idea. You wouldn't say "That may be good thinking, but it's not going to work because etc."
However, "good thinking" is sort of a popular idiom and is often used comically, or ironically, or sarcastically when someone does something really stupid. But it also may be used as a colloquialism among friends to mean "good idea."
Going out to dinner tonight could be an example of good thinking if doing so would solve some problem, such as killing two birds with one stone.
There's nothing in the house to eat!
Let's go out to dinner.
Good thinking.