Thomas is originally from Aramaic and means "twin". The general rule with baby names in Islam is that all names are acceptable unless they have a bad meaning. Since the meaning of Thomas is not bad, it is an acceptable name for a Muslim baby. Scholars generally do not recommend using names inspired by other religions, but this is only a preference and Muslims are not required to abide by it. The Prophet, peace and blessings of Allah upon him, had a wife whose name was Marya, which is the Coptic Christians version of the name Maryam/Mary. Even though the name was from a Christian background, the Prophet approved of it and did not ask her to change it.
For cultural reasons some Muslims may disapprove of using Western/Christian names, so you will have to be prepared to deal with their disapproval and having to explain to them that it is an acceptable name. From a religious standpoint it is a perfectly halal name.