As someone who has flown in and out of HND/NRT around 1000 times, I would offer the following.

1. Getting in and and out of the airport is about the same for either airport.

2. Travel time to Tokyo by train will be about 30 minutes longer for NRT.

3. I typically use Haneda when I can primarily because I use taxi/hire and HND is a lot cheaper.

4. If I were you I would consider the limo bus to the Tokyo Dome Hotel and then a shortish walk or taxi your hotel.

5. Second choice would probably be train to Tokyo station and then Chuo/Sobu Line to Iidabashi (need to walk across platform and change trains at Iidabashi.) From Narita some people will probably suggest Keisei line over Tokyo Express, which is also a good route.