Both mean something like "I'm very impressed with what you just did!". Not necessarily that "you are the best" at something, in spite of the word "rule" in one of the expressions which seems to imply a position at the top of some hierarchy. They're both used when, in the eyes of the speaker, the person receiving this compliment has just done something very cool / neat / helpful / skilled / otherwise awesome.

There really isn’t a difference. Though, I tend to hear “you rule” more from older people. I think it was most popular in the 1960’s and 1970’s.