Generally "Bandaraya" in Malay means City and that word is typically used to refer to highly populated areas managed by City Councils e.g. DBKL, MBJB, MBPJ etc. (see below for more details).
Smaller "Bandar" or towns are the next in rung and also apply to state capitals with a small population size so Yong Peng, Bandar Melaka, Seremban, Mersing etc these are all Bandar or towns.
Nusajaya is a brand new town and thats why it is called Bandar Nusajaya. Same like Putrajaya, it is also a town.
Interesting facts - The link shows how local governments are organised in Malaysia ->
http://jkt.kpkt.gov.my/en/main.php?...5&VertSectionID=43&CurLocation=43&IID=&Page=1
Each state in Malaysia is subdivided into many districts under the care of a local council or authority:
Majlis/Dewan Bandaraya (i.e. City Council) is the biggest and looks after city areas usually small areas with big pop densities. e.g. MBJB, DBKL (dewan bandaraya KL), MBPJ (Petaling Jaya), MBI (Ipoh).
Majlis Perbandaran (Municipal Council) is the next biggest and looks after suburbs within capital cities e.g. MPJBT (JB Tengah), MPKulai (Kulai), MPAJ (Ampang Jaya) etc.
Majlis Daerah (District Office) is the last type which looks after all districts not looked after by the above e.g. Majlis Daerah Yong Peng, Tangkak etc.