That's really up to you.

If we're looking at it purely from a public transit access perspective, my opinion is that transit from Haneda tends to be a bit crowded on both the monorail and the Keikyu Line. From Narita, it is a little bit longer, but the Narita Express or the Skyliner are more comfortable. You'll be dealing with trains and tickets either way. Similar story if you take a Limousine Bus.

However from Haneda, a taxi also becomes a viable option if you'll be staying in Tokyo proper. You won't be paying as outrageous a fare compared to trying to get a taxi from Narita to Tokyo.