Based off of a decklist by Gariel Nassif. Frank Lepore also had a Ninjas list a while ago and Ninjas (albeit a very different list) have appeared in Vintage too.
Apparently there was a Ninjas deck that just 5-0'd an online league, with a video here.
The main premise of the deck is to sneak in ninjas, like Ingenious Infiltrator, and generate lots of card advantage. To help get your ninjas into play, there are a bunch of evasive creatures, like Changling Outcast, Ice-Fang Coatl, Vendilion Clique, and Spellstutter Sprite that all have great ETB abilities.
Main Deck
Creatures
I want to draw special attention though to Changling Outcast - this card really pulls its weight. It can't be blocked, meaning you can rely on it to get a ninja into play. It's a fairy for Spellstutter Sprite, a wizard for Wizard's Retort, and, most importantly, a ninja for Infiltrator, allowing you to get a steady stream of card advantage.
Rounding out the rest of the creatures, we have Snapcaster Mage (yet another ETB effect, although having an unblocked Snapcaster will be difficult), Fallen Shinobi and Higure, the Still Wind at the top end, and Birds of Paradise for acceleration/fixing and is also another evasive creature to get ninjas in off of.
Nassif's original list had 4 Fallen Shinobi, which I'm not sure about. It does hit for a chunk and can steal some nice cards from your opponent, but you do have to get lucky with what it hits. I've been a fan of Higure since it was printed and I want to try it out in the deck. Being able to tutor for any ninja is good and being able to make your ninjas unblockable is also pretty nice. I'm really not sure what a good split of those cards would look like though and I really don't want to get too heavy on the top end of the curve. I'm also partially considering only having 1 Shinobi, 2 Higure, and then two other ninjas that Higure can tutor for, such as Throat Slitter, Okiba-Gang Shinobi, or Skullsnatcher (or Walker of Secret Ways, Mist-Syndicate Naga, and Mistblade Shinobi). Throat Slitter is nice creature removal, Okiba-gang is expensive, but may be good against control decks, and Skullsnatcher might honestly be good in the Uro and Mystical Sanctuary-dominated metagame. Honestly though, that might be too cute and just stick with the ninjas good in any circumstance. Nassif's original list also had 3 Plague Engineers, which isn't especially relevant in today's meta (with the exception of Humans and, on the rare chance, Goblins).
Non-Creature Spells
For non-creature spells, there's countermagic and removal. I'm not playing any Cryptics or Charms as those have very strict mana requirements and we're going to be playing spells or sneaking in ninjas on our turn, so we won't have lots of mana at our disposal on our opponents turn. So instead, I chose to include Force, Spell Pierce, and Wizard's Retort. They're all very cheap, flexible answers to our opponent's spells. I chose Wizard's Retort because we have 12 wizards in our deck (Changling Outcast, Spellstutter Sprite, Vendilion Clique, and Snapcaster) - I'm hoping that's enough to make it Counterspell consistently. I also toyed with the idea of using Familiar's Ruse so we can get back a creature with an ETB ability (like decks that are using Deprive to buyback Mystic Sanctuary), but I decided that overall it'd probably be better to keep a board presence and opted for Retort (although I'm definitely curious to try out Ruse). We also have Fatal Push as it's the best creature removal, Drown in the Loch as creature removal and another counter spell, and Abrupt Decay as an answer to Blood Moon, planeswalkers (Ashiok, Liliana, Wrenn, Teferi, etc.), artifacts (e.g. Chalice of the Void), and Uro.
Manabase
I'm always kinda guessing with the manabase, any suggestions are welcome! I have (only) nine fetches because I wanted to have more mana-producing lands because I'm a bit concerned about whether what I have is enough. I have Blooming Marsh as the only Fast land so that we can hit our one-drops with it. The rest are all basics and shocks and I'm really hoping that losing life from all the shocks won't be too much. I did (very briefly) toy around with the idea of using Sunken Hollow, but UB are the most important colors and I don't want to have two basics in play before I can fetch this into play untapped.
Other thoughts
Yes, I'm not playing either Arcum's Astrolabe or Mishra's Bauble although it very likely could be wrong. After watching enough matches, I've seen how powerful both of those cards are, but I'm not entirely sure this is the right deck for them. Bauble is busted with Emry and Astrolabe might open up the possibility of playing Cryptic or Charm. Honestly though, I don't know what I'd cut to include them or if including them is even the right thing to do. Happy to hear people's thoughts!
Sideboard
Pretty typical sideboard for today's meta: Ashiok and Nihil Spellbomb for Uro, Dredge, Kroxa and other graveyard decks; Ashiok and Damping Sphere for Titan, and Tron; Ashiok, Sphere, and Collective Brutality for combo decks; Brutality, Sphere, and another Drown in the Loch for red decks, Veil of Summer and Mystical Dispute for blue decks with countermagic; and Assassin's Trophy as a catch-all removal spell. I could see cutting Brutality and a Spellbomb for other cards that'll help in more difficult matchups.
Maybeboard
I discussed some ninjas for tutoring up already, so I won't repeat myself and I'll keep it brief. Other ninjas to consider are Throatseeker for red (dies too easily though) and Ink-Eyes, Servant of Oni (too slow and matchup dependent). I'm also really considering Faerie Seer again. I originally removed it from Nassif's list in favor of Outcast as I felt that Outcast was overall better, but being able to smooth your draws out with the Seer's Scry 2 (and of course it being another Faerie and Wizard) certainly is attractive. I'm just not sure what I'd cut. Other counterspells to consider are Spell Snare (is a dud against some decks), Remand (which maybe should be a mainboard card), and Aether Gust. I don't have any hand disruption mainboard as I envisioned this as more a positive tempo deck (i.e. I want to do stuff on your turn to slow you down). Maelstrom Pulse might be an interesting card to consider instead of Assasin's Trophy. It's slower and sorcery speed, but as Reid Duke always says, ramping your opponent always feels really bad. I'm also considering Jace, the Mind Sculptor. As with Cryptic and Charm, I don't really think this is the deck for Jace. He's very powerful, but quite slow and mana-intensive. Before Oko was banned, he (and Gilded Goose over Birds of Paradise) would have been an auto-include in this deck (but then again, which deck didn't auto-include Oko?). I thought about Mystic Sanctuary for a bit, but I'm not really sure this is the best deck for it again. We don't have anything really broken to bring back with it.
Closing Remarks
That's about all I have to say about this deck. I'd very much like to hear the community's thoughts and get whatever constructive comments I can!