Both can be used, see http://oxforddictionaries.com/defini
Many words that end with 'us' (Like Alumnus) has the plural form with 'i' (Alumni). So it is right to call HIPPOPOTAMI.
Actually, it's a Latin noun, to be more precise it's a second declension nominative singular. And the plural is obtained removing the -us and adding -i.
However given that it's in the language currently used (see Magdalena comment), you could build the plural following the English grammar rules as well, thus "hippopotamuses".
It's not Latin. It's Greek. Though it is second declension and it's not uncommon for English to use Latin second declension rules for Greek 2nd declension nouns and this is ok for Hippopotamus. You have to be careful with other words like Octopus though as pous is a third declension noun.so the plural would end in podes. Other examples of us not being latin 2nd declension nouns are genus (genera) and opus (opera), both 3rd declension neuter nouns.