If this was 4 years ago, the answer would be easy, hands down teh Honda Accord.
BUT, comparing 2011 models, the Sonata is, in my opinion, just as good if not better than the Accord. (by the way, I own an Accord, and love Hondas). If you are looking at 4 cylinder models only, I would really suggest the new Sonata 2.0 Turbo. It is a 4 cylinder with a turbocharger, giving you the performance of a similar V-6, but gas mileage more like a similar 4 cylinder.
Also, I suggest not getting a built in GPS navigation system. Like you siad, most of the time they bundle that package in with other options and it usually ends up costing thousands of dollars. Instead, just buy the car you like best and then invest in an aftermarket GPS such as a Garmin Nuvi.
Hyundai has a great warrantee, and the looks and quality are definitely right up there with Honda now, but I do not think you will be dissappointed in either choice.
My suggestion, test drive both, and chose the 1 you personally like best.
Last time I went car shopping, i was 99% sure of the car I wanted, but when I test drove it, it went to the bottom of my list. Testing them is the most important part.
GOod Luck