Like Moosey said I think トマス is closer to the most common pronuciation of Thomas. Incidentally 'Tom' would be written トム and pronouned Tomu (again with clipped vowel sounds)
Both are correct, and the only difference is the length of the 'o' If the o is short, as with Englih pronunciation, it it without the - If the o is long, as with the Dutch pronunciation, it is with the -