The ninjas are from a fake 80's videogame created for the movie, called Dojo Quest:
Here's an article about the licensed games in the movie:
The filmmakers licensed characters from real-world video games for the movie, but they opted to craft a fictional title starring a ninja-fighting heroine named Lady Lisa (played by Ashley Benson), who serves as an unconventional love interest for Gad's character. To promote "Pixels," Sony released a side-scrolling mobile game resembling "Dojo Quest."
"Lady Lisa was in the first draft of the script, and I thought it would be fun to create just one game that didn't exist back in the '80s," said Columbus. "It never occurred to me not to do it. I felt like we could get away with it. A character like Lara Croft could've worked, but I loved the fact that Josh Gad's character has been pining for this woman all his life."