Gregory Moulinet answers "neither", but if pressed would choose Beijing.
I lived in Tokyo for about 12 years and in Beijing for about 5. I left Tokyo for Beijing. I currently live in Shanghai. My answer to your question is ‘neither’… but if my choice was limited to these 2 cities and my work/life offering being perfectly equivalent, I would probably select (again) Beijing.
As most people pointed out, the biggest drawback living in Beijing is the pollution. That is the key reason I moved to Shanghai. Beyond that, the 2 cities are so different you will find good and bad things on both side and your choice will be determined by other factors than the cities’ features.
Choosing Tokyo instead of Beijing may seems a no-brainer considering the quality of services, internet ‘freedom’ and the visual/culinary esthetics of Japan. Talking Japanese is far easier to learn than Chinese among many other advantages that I am certain many will point-out and I used to appreciate greatly.
But…
These capital cities and their respective countries are currently taking a very different trajectory. China is generally progressing while Japan is taken into a slow spiral of regression which is painful to watch.
It’s easy to live well in Tokyo if you create your own comfortable bubble and blind yourself from the massive pile-up of social and environmental issues Japan is stacking against itself. By all means, choose Tokyo if you plan to live this way.
I personally prefer to be surrounded by optimistic Beijingers who have witnessed rapid positive changes and have become accustomed to try and integrate new ideas.
Beijing is not the rest of China and many massive, morally challenging (to say the least) problems are left to be addressed. The question is, do you prefer to be living in a place climbing rapidly upward or moving slowly downward? [Link]
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My comment: born in Tokyo, lived in Beijing and had frequent visits to Tokyo for business: I agree with Moulinet. One city is living (whatever horrid things that its government does), the other is dying but doesn't seem to know it
