1. The CN Tower is newer than the Empire State Building.
2. The CN Tower is younger than the Empire State Building.
3. The Empire State Building is older than the CN Tower.
[Which ones are grammatical?]
All are grammatically correct, but 1 is far better in wording than 2. The adjective "newer" is better for describing buildings (inanimate objects).
All three sentences you provided are grammatically correct. However, the word choice in the second sentence is slightly less common. The terms "newer" and "older" generally refer to the level of modernity, while "younger" and "older" are typically used when discussing age.
So, in terms of common usage, the first and third sentences are more frequently used to convey the idea that the CN Tower is more modern than the Empire State Building.