The North American ALMA archive query interface (http://almascience.nrao.edu/aq/) has security settings which prevent a user from uploading a list of sources or positions to query. However, the European (http://almascience.eso.org/aq/) and East Asian (http://almascience.nrao.edu/aq/) query interfaces do not have these restrictions, so you can use these to perform multi-positional searches.