Tokaigi (@Makuhari Messe or sometimes Ginza *please check) http://tokaigi.jp/2017/en/ In 2017 it was held on February 11th + 12th.
Anime Japan (@Big Sight): https://www.anime-japan.jp/en/ Tickets are usually available until mid-February. Tends to be held around March 23rd, Thurs-Sunday.
Haneda Anime Music Festival (@TIAT SKY HALL, Haneda Airport) http://www.haf.tokyo.jp/index_festival.html seemingly various events randomly strewn across March!
Niko Niko Chokaigi – (@Makuhari Messe) usually on the last weekend of the month
Tokyo Sandbox (Includes Tokyo Indie Fest) (@Akiba)
http://www.tokyosandbox.com/ Usually begins around May 10th in Akiba, with Tokyo Indie Fest happening on the Sunday.
Comitia – Usually on the first or second Saturday of May. ONE DAY ONLY!
One day only! https://www.comitia.co.jp/
Comiket Part 1 (夏コミ Natsukomi) (@Tokyo Big Sight) http://www.comiket.co.jp/index_e.html usually held around August 15th.
Tokyo Game Show (@
Usually around September 20th and runs for four days in total. Business days – usually the Thursday and Friday. Public days – the weekend.
Jump Festa (Shonen Jump festival) http://www.jumpfesta.com Seems to be held around 17th December.
Comiket Part 2 (冬コミ Fuyukomi) http://www.comiket.co.jp/index_e.html usually held around December 28th.
*** OUTSIDE OF TOKYO ***
May – Bitsummit (@Miyako Messe, Kyoto) usually on 20th May http://bitsummit.org/2017/
September – Kyomaf (@Miyako Messe, Kyoto) https://japancheapo.com/events/kyoto-international-manga-anime-fair/