Though it's changed a bit in the last few years with the slots opening and airlines like ANA opting to move some int'l flights to HND, NRT is still your best bet in terms of destinations, so it's still the best bet, logistically speaking, for transits. I haven't flown Haneda before, so I can't speak personally for amenities there.

Probably best to avoid transits that involve going from one airport to the other, but if you have to, remember to make sure that's factored in when it comes to time between flights, along with border stuff and what have you. There's a limousine bus that will get you there in an hour and change for 3100 JPY: http://www.limousinebus.co.jp/en/