Keep in mind this is my personal opinion and my experiences and I would like to start an active discussion in the comments.

Ninjas have been the most interesting class since launch and they have been very squishy but also very good at dealing effective destruction and have unique skill caps to them making everyone's personal ninja playstyle different. I have multiple catagories and will give an explanation to why which heros end up where they do and a weapon I recommend using with them. The catagories consist of AoE, Crowd Control, Single Target Damage, and Tankiness/Survivability (Often melee)

-AoE: For AoE I picked Dragon Scorch who has been at the top for a while. He gets Dragon Slash, Shurikens, and Smoke bomb. Along with these abilities he gets shadiw stance which gives him some extra tankiness. Right off the bat he really does his job well, he gets a huge dragon slash and shadow stance build which makes him be able to dive into waves and annihilate waves of husks. His smoke bomb his a good escape and AoE source of damage but if you play him well you should not use it too often. Just like Genji from overwatch he should dragon slash right after throwing shurikens(try to have max energy as he is not too efficient, boost towers help with this) he gets the job done, and using the best sword you have is good for the rush but before you get in tigerjaw can usually weaken the husks a bit.

-Crowd Control: For this interesting class I chose Slirmisher Edge who is my personal favorite hero. He gets Shurikens, Dragon Slash, and Crescent Kick. He gets his insane abilities to control the clumps and hordes of husks with his Dragon Slash solid upgrades and his crazy shuriken buffs which gives him a piercing 1/2/2. These already allow him to stay at a range while destroying any funneled husks. The dragon slash allows him to clean up any survivors of the shurikens with ease and if the husks start to get that close then a crescent kick can usually hit hard in the case of a mist monster that gets too far or a difficult wave the impact and overall damage stun keep the husks at bay once again, and usually if they get this far it is often time nice to get the reaper or elegant scythe and destroy them as you keep a lot of energy with this hero naking him ideal. If you have and upgraded turret holding 2 at a time possibly if you pair with an outlander like TEDD shot Jess you can cycle through turrets and bears when it gets rough. And if you didn't catch my weapon recommendation, I like scythes.

-Single target output: Explosive Assassin Ken, He is pretty simple, he gets assassination and makes explosions. If you need to take on a lot of mist monsters then he is a great choice and he does have AoE abilities so he isn't completely useless. He gets multiple assassination perks making him very deadly while getting off some of the AoE 'splodes. He deals the damage, destroys with laser swords, enough said.

-Durability: For durability I chose Neon Assassin Sarah who specializes with the neon scythe as it is literally her weapon, she gets abilities but her perks are the main focus as they massively buff scythe damage and allow for enemies to be ensnared much easier. She also gets a decent amount of life leech and with a health build from the beginning she becomes quite durable. She only works really well with the neon scythe orcthe reaper scythe but she is tanky enough to get the job done and her ensnaring abilities give her plenty of life leech.

These are my personal picks for the best ninjas for each damage type, feel free to disagree as I want to see what other players think of the list and ninjas as a whole.