No, trophies you've gained for games on PS3 will not carry over for the PS4. (This applies for all games)
Except that it doesn't apply for all games. There are a bunch of games that have one set of trophies that carry across PS3, Vita and even PS4. To answer the original question, we don't know at this point. There has been very little info released about the PS4/Xbox One and PS Vita versions of the games.