As everyone else has said, 'there are no flowers on the table' would be the better phrase.
Just to put a finer point on this question, the only time I would prefer the use of 'there aren't flowers on the table' would be in a negative response the the statement 'There are flowers on the table'. The reason being is that you mirror the word 'are' in the first statement to link the two statements together, making it clear you are providing a response to that statement.