I assume you mean the British Raj, becasue raj just means rule. The Maharajas were..... Maharajas. Maha means Huge, Extreme, superior and Raja means King. The Maharajas were the emperors of their state. The South Asia we see today isn't the same south asia during the early modern period, before the company established rule. A large chunk of it was part of a Mughal empire. But their rule was starting to come to an end as various revolutionary movements started to divide the empire apart. The British appeared around here when various empires dotted the sub-continent.

So as the British grew and gained influence/hostily tookover/bought a state, It absorbed it into the empire. That states Maharaja would then be made a British puppet. A leader only in image, most of the time they would choose the youngest son of a deposed king to groom in London to be a great puppet. Some states like the Marathas didn't get to even keep a Raja as punishment for a brutal war. Some like the Sikhs, got to keep their Maharaja and maintain puppet status. But were absorbed into British India once the crown stepped in in 1857.

Does that answer your question?