Tokyo and Japan on the whole have four distinct seasons and the impression you'll get can be completely different depending on when you arrive.
Our top choice: May or October for the best weather.
Also keep in mind: Winters (Dec-Feb) aren't as bad as you think - with dry weather and the best shot of seeing Mt Fuji.
When the plum trees start to blossom in late February or early March, it's the first sign that spring has arrived. The weather can be unstable in early spring, as there is an old saying that season has "three cold days and four warm ones"
By late March, the much awaited cherry blossom season arrives but when you can see it in Tokyo can vary depending on the year. In 2012 the peak viewing was around April 6, while in 2013 it was March 22nd (which was one of the earliest dates on record.)
If you're in town on the first week of April, you will see the blossoms somewhere for sure, though you may have to go a little north or climb to higher elevations find one.
In April, it's not uncommon to see the highs climbing above 20C(68F) making for a pleasant day outside. However you may want to avoid travel around Apr 29 - May 5 which is the long holiday period locally called "Golden Week". Virtually the entire nation travels during this period when planes and trains become packed. Hotel prices will also shoot up and you may be standing in lines for hours to get to your destined attraction. Car travel should be avoided - a drive to the Mt Fuji area from Tokyo can take 5-6 hours for example, double or triple the normal times! Things relax considerably after the Golden Week is over so if you can avoid this period, the spring is no doubt the best season to travel..
Great weather continues until early June when the rain season called Tsuyu arrives. It can rain the entire day for a week without any sunshine and the humidiy can stay above 90% making for unpleasant conditions. For example in 2017, June saw 20 days with precipitation. By early to mid July, just when the schoolkids enter summer break, the Tsuyu is finally over and summer is officially here. While there are many festivals and fireworks shows in the summer, you may find that the climate is similar to that of a tropical area such as Singapore or Bangkok. The temperature sometimes reaches 35c (95F) and remains above 25c (77F) even in the nighttime. You may want to plan some indoor activities such as shopping or a visit to the museums during the daytime to avoid the heat.
In September, things finally start to cool down a bit, and conditions should be preferable for sightseeing. However you do need to watch out for typhoons that occasionally make landfall during this time of the year although the storms usually pass through quickly without causing any serious damage.
By November, the leaves will start to turn colors in the areas up north such as Nikko and Hakone but it is usually not until the first week of December when you can see like the photo to the left in central Tokyo.
Tokyo has a fairly mild winter, at least compared with many European cities. In the afternoon, temperatures may rise to around 10℃ while the lows rarely dip below the freezing mark. Skiing can be enjoyed in the mountains of Nagano or Niigata about 2 hours north, but snowfall in the city is extremely rare. December - February is the driest months of the year and it is not unusual to go weeks without any precipitation. Visibility is the best in winter, meaning chances of seeing Mt Fuji is the best this time of the year.
Be aware that many museums close for the Year-End/New Years, from around Dec 28 to Jan 4, although shopping malls generally stay open. Trains continue to run as normal. Many workers in Tokyo return to their hometowns for the holidays so the long distance trains and flights can become fully booked.