Actually Shibuya probably has slightly easier access to Narita and Kyoto, but not by a big-enough margin to make a difference. Shibuya might also be better for bars and restaurants, and you're closer to Ebisu, which has a very good selection of restaurants. Based on your NYC interests I doubt if you'll want to spend much time in Roppongi.

Shibuya Dormy Inn is actually in Harajuku, which may be the nicest location for your interests.