A caliphate is the traditional form of government within Islam, arguably the only form of government permitted to exist according to Islamic law (sharīʿah). The term caliphate comes from the Arabic word khilāfa, meaning "succession" or "representation." Thus, a caliphate is an Islamic polity succeeding the Prophet Muhammad, with the caliph as the technical successor or representative. Historically, caliphs had both political and limited religious authority - they could establish what was already revealed in the Qur'an and the Sunnah, but could not have any form of religious revelation of their own. Within Sunni Islam, caliphs were therefore never viewed as religious figures; rather, they were understood to be the heads of state and the ultimate decider (for a time) on the legal ramifications of a Qur'anic verse or prophetic text, with the counsel of the most knowledgeable Muslims. With respect to Shi'i Islam, the only historically recognized Shi'i caliphate to have existed is the Fatimid caliphate; the Fatimid dynasty differed from typical Sunni caliphates in that the caliph was viewed by fellow Isma'ili Shi'is as having a unique understanding of the secret meanings of the Qur'an. But as a whole, caliphs were originally seen as having authority in all political/military/legal affairs, and only some religious affairs.
A sultunate is a form of government with a sultan as a political and military leader; it is essentially equivalent to an emirate (there is no real difference between these terms). The term sultan was first used as a title of authority by Mahmud of Ghazni in 1002. He declared himself Sultan of Ghazna, yet still maintained his allegiance to the Abbasid caliph. The 9th century witness the fragmentation of the Abbasid caliphate and the rise of multiple sultunates and emirates, yet these sultans/emirs always proclaimed their allegiance to the caliph, since the caliphate continued to be viewed as a religious obligation. Sultans only had power with regard to political and military matters - religious/legal authority was eventually acquired by Islamic scholars. So after the 9th century, the "caliphate" was viewed as an umbrella of multiple polities with sultans and scholars at the center of power. This changed once the Ottoman sultans defeated the Mamluks in 1517 and assumed the title of caliph - after this point, the title of sultan was "joined" with the title of caliph.