Because of the dynamics of how a ship moves in water, the most stable part of the ship is as low as you can go and as close to the middle as you can go.
I spent 6 years in the Navy and those ships are made for speed and maneuverability, definitely not for comfort, so they do not have stabilizing devices as those create too much drag.
Cruise ships, especially the newer ones, have stabilizers to help with the movement. The stabilizers on the newest ships are computer controlled and quite an amazing device.
There are basically two types of movement on a ship; rocking and rolling, as I like to call it. The rocking motion is from side to side. Best place to be on a ship to counteract this is as low as you can get. Unfortunately, if you want a balcony or a suite, you're going to be up higher.
The rolling motion is when the ship goes over the waves from front to back or back to front. This type of motion is felt more in the front of the ship than anywhere else. This is the worst place to be if your subject to motion sickness.
The back of the ship will feel less rolling motion, but sometimes can have vibration from the propellers. This vibration will vary by ship and design as many of the newer ships have azipod propellers and these create alot less vibration than the standard type of propellers. On some older ships, the back of the ship can have some fallout from the stacks, but this has disappeared with better designs over the last 15 years.
Now, with all that said, for first time cruisers who don't know how they may handle any motion, it's best to be as close to the middle of the ship as possible. This will find the least amount of motion. If you want an aft cabin because of the view or the larger balcony, that would be the second best option. This is why all restaurants on ships are either in the middle or the back of the ship.