All are correct, but there are some subtle differences:
Shall we meet - sounds slightly formal
Are we meeting? - this would be used more for inquiring as to whether or not a group is going to meet, not as a request to meet.
Are we going to meet? - this sounds like asking if something is going to occur, not a request
If you want to ask to meet someone I would phrase it as "do you want to meet?" Or "should we meet?"