Surprisingly, Ninjask performs better in Ubers than in OU, due to the preponderance of Psychic- and Dark-types and the lack of dedicated phazers in the former tier. However, using Ninjask does come with its share of problems: if the opponent sends in Groudon or Lugia, you'll definitely be starting the match off on the wrong foot, so your team should be able to handle them. But otherwise, you'll be surprised at how easy it is to pass to a sweeper and potentially run through an opponent. With some planning, carefulness, and a bit of luck, Ninjask can be a real asset to your support-oriented team.
While Ninjask is often bashed for its alleged uselessness in OU, it finds a unique niche in Ubers as a lead. This bug is able to pass Speed (and maybe even Attack) boosts to sweepers such as Dialga and Rayquaza far more easily than it can in OU for a number of reasons. For one, all Ubers Taunt users, being Psychic- or Dark-type, are 2HKOed by X-Scissor, meaning that Taunting Ninjask is risky. For another, there are only 3 commonly seen phazers in Ubers: Groudon, Latias, and Lugia. Latias is 2HKOed by X-Scissor, and the others are easy to set up on by Taunt users of your own.
The first move you should use is Substitute, unless facing a Deoxys-S or Mew lead; use X-Scissor instead on their expected Taunt. The only move that is up for debate is the move in the second slot. Swords Dance can be used if a switch or a support move is predicted, and it can potentially result in a sweep. Finally, Protect can be used to help you outpace and defeat TrickScarf Darkrai leads by setting up a Substitute, and gain Leftovers recovery.
Liechi Berry guarantees that you will pass at least one Attack boost to a sweeper, while Leftovers is a reliable choice to help you set up more Substitutes and pass off more Speed. The EVs for this set are very carefully chosen. 108 Defense EVs ensures that an ExtremeSpeed from Lead Rayquaza and Deoxys-A max out at 74.90%, meaning that you can put up a Substitute and Baton Pass away +1 Attack and +1 Speed (and give your sweeper a crucial free switch-in), more if you have Protect. 176 Speed lets you outspeed Deoxys-A leads, and 226 Attack EVs ensure that every Taunt user is 2HKOed by X-Scissor.Team Options & Additional Comments >>>
This set takes a risky approach to support the team, but if it is successful, the results can be game-breaking. You can potentially pass +2 Attack and +2 Speed to your recipient, who can then easily sweep the opposition. However, this set is more easily stopped by priority and status than the first set due to the lack of Substitute, so you will need to play carefully, especially if you choose to run this set as a lead.
On Ninjask's first turn in, you should use Swords Dance while the opponent attacks, using Baton Pass afterwards. If you are facing something faster, such as a scarfed Shaymin-S, you should use Protect first to ensure that the opponent doesn't get lucky with a flinch from Air Slash. Then use Swords Dance and pass to a recipient that can handle the attacks being thrown your way. If you anticipate that your opponent has multiple phazers (likely the case on a stall team), avoid using Ninjask until said phazers are neutralized, either by fainting them or using Taunt.Team Options & Additional Comments >>>
Other than the aforementioned sets, there is little that Ninjask can do. As a Choice Bander or Life Orb user, it has very poor coverage, relying on Dig to hit Steel-types such as Dialga. You could try a Choice Scarf set, but Ninjask, who is faster than Team Rocket and the speed of light, can't make good use of it.
Checks and Counters
Groudon and Lugia stop Ninjask from Baton Passing anything due to Roar or Whirlwind. Giratina also has access to the phazing move, but it rarely carries it. Wobbuffet can force Ninjask to Baton Pass lest it be Encored.
Scizor is a great priority user, but if you have to switch it in, then the Ninjask player has a free Substitute, and can Substitute down before passing to Dialga, Palkia, or Groudon, which can be deadly. Other than that, ExtremeSpeed users are a good idea, but lead Ninjasks are EVed to deal with ExtremeSpeed, so you'll need prior damage on it to succeed.
Trick Room makes Ninjask fairly useless, to say the least, but requires a team built around it to succeed. Other than that, you can Explode on or attempt to cripple Ninjask's recipient in some way, but this takes prediction, and if you switch, you may have given the Ninjask user a free turn, which is never a good idea. In short, you should seek to apply pressure on Ninjask and deal with the recipient if you don't have any surefire ways to stop the bug.