I am a big fan of the Taurus as I have owned all three iterations on the Volvo D3 platform - a Five Hundred, a Sable, and the current generation Taurus. My parents have a Lincoln MKS. My cousin has a 2004 Lincoln Towncar Signature, so I am familiar with the ride in that. I haven't tested either of the GM cars in their current incarnations - I've owned and driven a W-Body Impala and an Epsilon-II Malibu, and one would never describe their seats as comfortable.
Based on that experience:
The seats in the Taurus at the top trim are like the seats in the Lincoln MKS. They are very comfortable. I drive in bumper-to-bumper commutting trafic as well as 5-7 hour trips to visit customers over the midwest. I have had no complaints. When driving with colleagues, they have wanted to take my car instead of theirs (an Acadia, a Dart, a Dodge Durango) citing ride comfort.
The only thing I would change if I was maximizing comfort - with my current Taurus, I have the 20" wheels. I had the 18" wheels with my previous iterations. The 20" wheels make for a more "sporty" feel, so you will feel the ride more on broken pavement. The previous ones were more capable of swallowing the bumps on broken pavement. If you want to maximize comfort, go for the smaller wheels, or swap them with aftermarket wheels.
Compared to the Town Car: A Town Car is its own kind of comfort. In the Taurus, you will sit much more upright. I believe Ford adopted this from their dalliance with Jaguar. When I get in a Town Car, I just have this sensation of sitting down into it with my feet straight ahead. You will be driving with your legs at a much more seated-in-a-chair position. It's not an SUV experience, as you don't step up into the seat. I like to sit upright more.
One suggestion: Consider the Lincoln MKS. The used MKS is about the same price as the Taurus, and Lincoln made it just a little bit nicer in all the creature comforts. It is very smooth, even with 20" wheels. You can also get the EcoBoost V6 in the MKS.