What was the hierarchy system among Mauryan queens?

Agramahishi/Pattarajmahishi was considered the Chief Queen of the Emperor. She gained a salary and had the right to sit next to the King and even participate in the administration as long as the King allowed.

Durdhara was Agramahishi of Chandragupta Maurya.

Dharma is called Agramahishi of Bindusara in Mahavansh Tika but she was a commoner in Ashokavadana.

Asandhimitra was Agramahishi of Ashoka and after her death Tisyarakshita was given the post till she burnt Kunala’s eyes and Ashoka tortured and burned her alive in his torture chamber.

Then there were Devis who were ladies of good and noble lineage and their children had right of inheritance, Darakas were also secondary wives and then there were Bhoganyas who were pleasure women and kept only for physical satisfaction.

Mauryans Empire also had Ganikas (Courtesans) and Dasis (Megasthenes denies this but Arthashastra explicitly mentions slavery system).

Who was queen during Akbar's reign?

Ruqayah Sultan Begum

Ruqayah Sultan Begum was the first wife and Chief Consort born of Mughal blood. She was daughter of his uncle Hindal Mirza.

Salima Sultan Begum

Salima Sultan Begum was daughter of Akbar's paternal aunt Gulrukh Begum. She was first married to Bairam Khan and after his assassination Akbar married Salima.

Maryam Uz Zamani

Maryam Uz Zamani was daughter of Raja Bharmal of Amber and she was married to Akbar as a strategic alliance and safety of Amber. She became mother of Waliahad Salim who ascended the throne after his death and took the name Jahangir.

Arif Un Nisa Begum

One of the lesser known wives of Akbar. Her origins are not known. Her portrait simply says Zauja Akbar Padishah means wife of Emperor Akbar. Her portrait shows her holding a sword depicting her strong personality.

He had several other wives as well.