Pylons came out first. Some are made into the boat and others are aftermarket or extended and have cables that run from the pylon around the bow of the boat to hold it in place when under a load. These lines can get in the way especially if you have a crowd with you or an open bow boat. When you store an aftermarket pylon you have to remove if from the base and remove the cables. This generally leaves the base in the floor and personally prefer the floor to be clear. However, this allows it not to be permanent. If you have a pylon you may notice an uncomfortable amount of flex when pulling a larger person especially when they edge out. Some people say this is because all of the force of that weight is applied to one place and the flex can be reduced with a tower because you have the weight dispersed over 4 mount locations.
Towers are a little more expensive than pylons. A tower allows you keep your seating room and there are no cables to run to the bow. You can mount board racks, speakers and lights on it. Plus with most towers you can run your wiring through the tubing. Now some towers are not very tall so if you are above average height you may hit your head especially if you have hanging accessories. On the bright side there are some manufacturers like Big Air and Vulcan that make their towers about 5 feet tall. This means with an average gunnel (2ft) your at about 7 feet, so most people don't have to worry about hitting their head.
To be honest a lot of this argument has to do with personal preference. Some people say "if it ain't broke don't fix it" and prefer the slightly less expensive and less permanent pylon. While others prefer the more permanent and clean approach of a tower. Below is a list of forums that have discussed this topic. Keep in mind the forums are a little dated so the prices are a little off.
Skylon Pro XT Tower