It is more common to say 'by noon tomorrow'. For example:

'I will be finished with work by noon tomorrow.'

However, you will also occasionally hear the phrase 'at noon'. For example:

'I will pick you up at noon tomorrow. See you then!'

'By noon tomorrow' is the usual phrase.

'By tomorrow noon' is not wrong, but it is more unusual. It has an old-fashioned sound to it.

How about "by the noon time of tomorrow"? 

I also wanted to add that it is incorrect to say 'by tomorrow noon'. You will never see or hear this phrase.