We are visiting at the same time
 

We are just back from 3 weeks in Japan having visited Mie Prefecture, Nagoya, Niigata and Isawa.
The weather can be mixed at the end of March/April. Over the last 15 years we have had varied weather, lots of rain around Tokyo, snow in Niigata, cold days and wonderful Spring days. Pack layers and a good waterproof. We found the best Sakura has been the first week in April in Tokyo/Isawa.
This year we are doing Tokyo, Niigata for the koi, Fuji area and last of all Isawa.

Sue McCann
YOUR KOI

Definitely bring some clothes for cold weather, not only warm. I have seen it snow during cherry blossom season in Tokyo more than once- be prepared for temperatures under 10 deg C as well as up to 20 deg C. It's a very changeable time of year.