...PvE - doesn't matter. Just a DPS race, so take whatever. It's too stupidly easy and mind-numbingly boring to be of enough challenge to consider this level of micromanagement and be taken seriously.
...PvP - My vote is on the Runabout. Tractors help in PvP considerably with how often 4 of those things will proc. Combine that with the 360 degree phaser arrays they have for phaser procs (particularly when you and your team run phasers as well) and you get a good number of enemy subsystems knocked offline in a match.
If you're running a healer Atrox, I'd consider shield repair drones.