Really like the use of Phage and Sun Quan. Cobbled Wings, Blight Keeper, and Contraband Kingpin don't seem that efficient. Another card you could try that makes your ninja bigger like Sai of the Shinobi is Ambuscade Shaman. You could also try Sword of the Animist for more ramp.

I made a Vela deck that features ninja and Eldrazi instead of pirates. Do check it out if that sounds interesting.

Eldrazi Ninja Scroll

Commander / EDH elgosu1337

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Hi High_Priest_of_Avacyn,

I like that third combo you're mentioning. I'm going to steal it for my deck.

Regards,

NV_1980

elgosu1337 and NV_1980

I've made some changes if either of you are interested. I'd love to hear some more feedback.

High_Priest_of_Avacyn

Ronin Warclub and Puffer Extract work with Ninjers.

Cybersix

I have considered Ronin Warclub, but decided against it because it wasn't a "may" effect to attach it to every creature I play. As for Puffer Extract I can see the use and it could be a finisher late game, but I don't think it really fits with what I'm trying to accomplish with this build. I do appreciate the input though.

High_Priest_of_Avacyn