Those three bikes are all very similar and your decision should be based on fit first followed by personal preference. Some of the things people notice between bikes: shifters. Take a test ride and do a lot of shifting. Do your hands prefer one over the others? I also recommend a long enough test ride so that you can try the entire range of gears. The Kona has an 11-34 cassette in the back and I hate mine. The gear spacing, compared to my 12-25, is very large. The difference will be very noticeable on the large front ring, but may not be too bad on the middle ring. The other two bikes have 11-32 cassettes. The tire sizes are similar: 32 or 35 so not much difference there. The Trek has a higher price tag than the other two, but I don't think you get more bike than the Kona or Giant. All three bikes are popular choices and you won't go wrong with either of them.

I know you asked about these three bikes, but I've been seeing so many posts in the last few weeks where people love their Jamis Coda Sport. You might want to look around for one of those and try it out. It's a steel frame bike, which might give a smoother ride.