Sure you can. I think you can just put New York City in the search box instead of a specific airport to show all the NYC airports (JFK/LGA/EWR) but if that doesn't work you'll need to use the "Include nearby airports" option from AA's advanced search page. Just chose a return to EWR instead of LGA.
edit: You can put NYC in as the origin and MIA as the destination and it'll let you book a round trip using flights between the NYC airports and MIA without having to do the multi-city thing.