"Best actor" is a rather nebulous term. All depends on what wou think makes a good actor - presence, charisma, range, believeability, power...
IMHO:
TOS - DeForest Kelly, for adding humanity and passion to what started as a fairly simple role. Probably one of the best examples of an actor shaping a character.
TNG - Stewart. The dominant presence on the screen [and off it as well, going by some stories]. His dignity and power was great for the position of Captain, but also opened dramatic possibilites (adding to the impact of scenes where he breaks down) and led to comedic moments.
DS9 - Not really a standout here. I think the recurring guests like Fletcher, Alaimo and Robinson were as good as any cast member. Meaney is the obvious choice along the same likes as Kelly.
Voy - Jeri Ryan. Maybe the strongest cast, but Ryan was just stunning in a lot of roles - excellent as a full Borg originally, excellent as Seven normally and outstanding when called upon for a greater range such as in Infinite Regress. Also home to the best guests, such as Joel Grey, Andy Dick, Michal McKean, Lori Petty and Brad Dourif.
Ent - Trinneer. Droll, charasmatic and likeable.