I went four times to Tokyo for business and my four three-weeks stays have included what the Japanese would call the full experience - a thyphoon, cherries flowering, snow, an heat wave in early September, several earthquakes including the March 2011 big one, and even a small bit of radioactivity from Fukushima.
Tokyo is an incredible metropolis, very safe, at times very confusing (understanding the patterns of metro and private railways interchanges is not easy, and getting lost in the Shinjuku station is also quite easy). Do not expect English to be widely spoken, and even if spoken it is not understood; but you can manage on your own somehow. Shopping is incredible and probably the best part of walking around. There are not so many thing to see - I tell this as I live in Italy where there are so many antiquities to see - but the incredible thing are the very Japanese people and trying to understand their way of thinking. Japan is safe not only because there is a lot of police around - mostly helping everybody and giving directions - but because the society is so structured and polices itself.
As you are considering Argentina and Chile as well: my business brought me also in Santiago once and Buenos Aires two times. Santiago is somewhat a somber and grey city, but for the quarter with the Neruda home. Chileans are somewhat the Germans of South America - the organization is not as bad as in other places and there are not so many poor people around. A postcard made from Santiago to Italy in a few days. But a fellow in my group had his suitcase stolen while we were boarding a bus.
Buenos Aires could be one of the great capitals of the world had not been destroyed by bad politics in the last fifty years. The opera house and the Ateneo bookshop, memories of a bygone era, are astounding. The people are very bright - only in London and New York you can find as many theaters and music places - but the city is very run down. Personal safety is not a concern but making it without being separated from your money or your belongings may be - locals told us to be careful with our suitcases as they get easily stolen. A postcard was very difficult to send - you can buy stamps only from post offices, good luck to find one of them open - and it took four months to reach Italy.
I would go to Japan first.