Ray Lazier Lengend, 40, faces a maximum sentence of life in prison on hate crime and arson charges.
He told police authorities that he attacked the centres over the weekend as he believed Muslims were trying to take over his life.
Lengend, a naturalised US citizen from Guyana, is currently being held in a Manhattan hospital where he is undergoing medical treatment.
According to a court document provided by the Queens District Attorney's Office, Lengend told police "in response to being asked why he would attack a mosque, the defendant stated that he hated all the Muslims and Arabs because they were trying to take over his life. They have been doing it for 40 years".
Lengend has been arraigned and is being held without bail.
He has told police he wanted to "inflict as much damage as possible and take out as many Muslims and Arabs as possible" by throwing firebombs at them.
The unemployed truck driver hurled the firebombs at five locations across Queens near here on New Year's day, including at an Islamic centre, a home that housed a temple and a convenience store.
He had also cited personal grudges for not being allowed to use the toilet at the centre and for being thrown out of the store for shoplifting as reasons he was upset with the owners of the place.