¥20,000 is around $166. I don't think most people recommend the train *only* because of speed, but also cost. The Skyliner for three people is ¥7,410, which is still significantly less than ¥20,000.

If you're ok with the cost, then by all means, take the car. The travel time is going to be around the same. The convenience will be a lot better with the car. It's just going to cost more. I personally would have a hard time stomaching $166 just for a ride from the airport to my hotel, but different people have different financial scales and different ideas for what each part of their trip is worth.