“Like night and day” means “very different”.
A. Where’re ya from?
B. New York.
A. Ya like Tokyo?
B. It’s OK–too crowded, rushed… noisy?
A. New Yorkers are used to it!
B. I’m from Long Island.
A. But Tokyo and New York are similar.
B. Like night ‘n day.
B. We don’t run into each other. We have more space; it’s quiet.
Here, speaker B is expressing an opposite opinion. She probably likes Japan–and Tokyo too–for their own qualities… but like many Americans–and especially New Yorkers–she feels it is best to share her true feelings: She doesn’t think Tokyo and New York are similar (at least in the ways she explains that they are different)–in her opinion. And in her use of the expression, like night and day, she is perhaps being a bit sarcastic (saying the opposite thing-with other words), rather than directly contradicting speaker A and saying “no they are not similar”. The complete unspoken–or suggested comment–would be: “Yes, they are similar–like night and day are similar,” meaning “night and day are similar because they are parts of the day, but one is dark and one is light–so they are not similar at all!”