All things being equal, I'd say it will depend on your use. I put thrusters in both my 1:100 Engel Typhoon and also in one of my big 66" Nautilus builds. There is some pretty good video of the Nautilus running here:http://www.youtube.com/watch?v=i_vGTUlCQq0
Skip to 1:25 to bypass the OTW Dive Module overview.
No one is going to use a Graupner style thruster to steer at speed, let's be realistic. They're for maneuvering at low speeds or while docking. Both of my thrusters were bow-mounted, but that was more for practicality than anything else. There was simply more room up front that in the rear with all the linkages and drive shaft. I think that a rear thruster would make more sense, personally. That way if you're docking you can just point your boat at the dock (or pond side or what have you), ease in to a stop, and then thrust the stern in for a perfect docking. With the thruster in front, you'd have to reverse in for the same effect.
Solve the dilemma and just put two in! That would make for some pretty cool pirouettes underwater!
I think I remember that the real Typhoons actually had a drop down thruster pod. That would be a great thing to engineer for a scale boat. Just have it permanently dropped for simplicity if you wanted, tied to your rudder linkage for left/right steering. Have it power on when your rudder is hard over to either side.