The Stage Version: "Cool" is in Act 1, "Gee, Officer Krupke" is in Act 2, and "I Feel Pretty" is after "The Rumble."
The Movie: "Gee Officer Krupke" is in Act I, "Cool" is in Act 2, and "I Feel Pretty is before "One Hand, One Heart."

People tend to disagree over which organization is better for the overall storytelling. A lot of people think that the movie's organization is better because the second act is darker, and "Gee, Officer Krupke" and "I Feel Pretty" are too light and break the mood, especially when you consider how tragic "The Rumble" is. Others say that the stage version is better. "Gee, Officer Krupke" keeps the mood from getting too depressing by providing comic relief. Some may say that it's out of character for them to be joking around since Riff just got killed, but others could argue that making jokes is the way that some people deal with loss. Also, having "Gee, Officer Krupke" later in the show makes West Side Story more like Romeo and Juliet, which has a similar comic relief scene at that point in the story. As for "I Feel Pretty," some people might find it odd for Maria to sing a happy song in the scene after her brother was killed. Others would say that it adds an element of irony when you consider that she doesn't know what has happened and is obliviously singing happily. I can understand arguments on both sides. I have mixed feelings, so I can't decide which organization is better storytelling. What do you think?

It's such a subjective issue, I'm not sure which version I prefer, but...

I recommend this essay, "What's the Difference"?

http://www.wssonstage.com/Difference.html

It beautifully details and analyzes every difference between the film and stage versions. I like it because even though the author clearly has strong opinions, his attitude is neither "stage rules, movie sucks" nor vice-versa. He obviously has a deep love for both versions, yet acknowledges the flaws of both too, and prefers the movie in some moments, the stage version in others.

His views on the "Krupke"/"Cool" issue are especially interesting - he considers both songs more effective when placed after the Rumble and thinks the movie might have been stronger if "Krupke" had been cut.