But you forgot the best tool of all of them Apples Migration Assistant and its free!
OK, here's how you can do this as you have two macs you'll need to connect the two via Ethernet or FireWire. You can even go directly back to back (no hub required). Then use your HD docking station to hold your new HD and connect into your MacBook Pro. I would recommend getting a FireWire case as it will be much quicker than the slow USB2 ports it has unless you have a PC-Card with USB3 ports. Then setup your system in Target Disk mode and then run the app.
As for your other cloning utilities:
You may want to make sure you have the newest versions and double check to see if they are multi-threaded so they can leverage the dual cores of your systems CPU's. I've had problems with Super Duper so I won't use it the other two are both OK. I use Drive Genus personally and have had good success with it.
In any case you really don't need the docking station as you can use your iMac in Target Disk mode in order for the clone software to clone the files (the cloning software can't copy opened files) to your other drive but this time using a Firewire cable between the two systems (much quicker than the USB dock with either USB2 or USB3).
Basically you have Apples migration assistant and the cloning software which all do the same thing here. The ease and speed of each is different. As to the hardware side of things by leveraging your systems built-in abilities (Target Disk mode) and a FireWire case you don't really need the slow USB docking station. If you are going to do it that way I would recommend getting a USB3 PC-Card that fits into your MacBook Pro (thats the hatch on the left side) which will speed things up.
As to your last question: Yes you will need to clone the entire disk so all of the permissions are carried over. If you use Migration assistant your in-fact Copying Vs Cloning but Apples tool also brings across the permissions like the cloning software. So if you have some stuff you have already on your disk you might what to use it instead.