Q. Is it correct to call Brahma, Vishnu and Shiva as the Trinity? (knowing that Brahma came from Vishnu's navel and Shiva came from Sankarsana)
Brahma, Vishnu and Shiva are qualitative incarnations of the Supreme Personality of Godhead, technically called `guna avataras'. They are in charge of the three qualities or modes of material nature viz. passion, goodness and ignorance. In that sense, it is right to consider them a Trinity -- in charge of creation, maintenance and destruction of the universe, respectively.
`Trinity', however, is generally a misleading term as it is often used and understood as indicating three aspects of the same Absolute, which is a conception or terminology borrowed from Christian teachings. This understanding is not fully correct. Although Brahma and Siva are incarnations from Vishnu and, as you have mentioned, they have their origin in Vishnu, both Brahma and Shiva are in a different category ("tattva") altogether, and it is important to understand this distinction.
Krishna is the source of everything, the original cause of all causes. Thus He is the Absolute, and source of all incarnations. But Brahma is actually a living entity ("jiva tattva"), just like any one of us, but he is specially empowered by the Lord for the work of creation. Any qualified living entity can occupy the post of Brahma. Lord Shiva is not an ordinary living entity, in fact he is altogether within a different category ("siva tattva") than living entities. However, he is not in the Vishnu category ("visnu tattva") either. He is in a special category of his own. Thus Brahma and Shiva cannot be considered on the same platform as Vishnu. Of the three, Vishnu alone is understood to be beyond the control of material influence.